rs6897690

Variant names:

• chr5-142321387-A-G
• rs6897690
• NM_001127496.3:c.-48+3457T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-142321387-A-G
• chr5-142321387-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001127496.3(SPRY4):​c.-48+3457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,184 control chromosomes in the GnomAD database, including 48,959 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (48959 hom., cov: 32)
• Consequence: SPRY4 NM_001127496.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 3 publications found

Genes affected

SPRY4 (HGNC:15533): (sprouty RTK signaling antagonist 4) This gene encodes a member of a family of cysteine- and proline-rich proteins. The encoded protein is an inhibitor of the receptor-transduced mitogen-activated protein kinase (MAPK) signaling pathway. Activity of this protein impairs the formation of active GTP-RAS. Nucleotide variation in this gene has been associated with hypogonadotropic hypogonadism 17 with or without anosmia. Alternative splicing results in a multiple transcript variants. [provided by RefSeq, Jun 2014]

SPRY4 Gene-Disease associations (from GenCC):

• hypogonadotropic hypogonadism 17 with or without anosmia

  Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics
• hypogonadotropic hypogonadism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Kallmann syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001127496.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4	NM_001127496.3	MANE Select	c.-48+3457T>C		intron	N/A	NP_001120968.1	Q9C004-1
	SPRY4	NM_030964.5		c.-29-1593T>C		intron	N/A	NP_112226.2
	SPRY4	NM_001293289.3		c.-109-1593T>C		intron	N/A	NP_001280218.1	Q9C004-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4	ENST00000434127.3	TSL:1 MANE Select	c.-48+3457T>C		intron	N/A	ENSP00000399468.2	Q9C004-1
	SPRY4	ENST00000344120.4	TSL:1	c.-29-1593T>C		intron	N/A	ENSP00000344967.4	A0A0C4DFS6
	SPRY4	ENST00000921739.1		c.-4374T>C		5_prime_UTR	Exon 1 of 2	ENSP00000591798.1

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121675 AN: 152066 Hom.: 48904 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.791

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.800 AC: 121786 AN: 152184 Hom.: 48959 Cov.: 32 AF XY: 0.803 AC XY: 59713 AN XY: 74398

African (AFR) AF: 0.829 AC: 34431 AN: 41540

American (AMR) AF: 0.825 AC: 12619 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2677 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5068 AN: 5184

South Asian (SAS) AF: 0.839 AC: 4054 AN: 4830

European-Finnish (FIN) AF: 0.778 AC: 8215 AN: 10564

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52208 AN: 67988

Other (OTH) AF: 0.794 AC: 1675 AN: 2110

Alfa AF: 0.774 Hom.: 76345

Bravo AF: 0.807

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.57
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6897690; hg19: chr5-141700952; COSMIC: COSV59985586; COSMIC: COSV59985586;