ENST00000432677.2:n.48T>C

Variant names:

• chr5-142745612-T-C
• rs7732591
• ENST00000432677.2:n.48T>C

Variant summary

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

The ENST00000432677.2(SPRY4-AS1):​n.48T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 398,052 control chromosomes in the GnomAD database, including 21,703 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 0.33 (15822 hom., cov: 32)
  • Exomes 𝑓: 0.16 (5881 hom.)
• Consequence: SPRY4-AS1 ENST00000432677.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 8 publications found

Genes affected

SPRY4-AS1 (HGNC:53465): (SPRY4 antisense RNA 1)

LINC01844 (HGNC:52660): (long intergenic non-protein coding RNA 1844)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432677.2. 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
	LINC01844	NR_110558.1		n.13T>C		non_coding_transcript_exon	Exon 1 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRY4-AS1	ENST00000432677.2	TSL:1	n.48T>C		non_coding_transcript_exon	Exon 1 of 4
	SPRY4-AS1	ENST00000652722.1		n.26T>C		non_coding_transcript_exon	Exon 1 of 5
	SPRY4-AS1	ENST00000652991.1		n.60T>C		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49958 AN: 151968 Hom.: 15761 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.0875

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.160 AC: 39420 AN: 245966 Hom.: 5881 Cov.: 0 AF XY: 0.154 AC XY: 19201 AN XY: 124624

African (AFR) AF: 0.808 AC: 5774 AN: 7148

American (AMR) AF: 0.279 AC: 2074 AN: 7432

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 1391 AN: 9222

East Asian (EAS) AF: 0.365 AC: 8359 AN: 22890

South Asian (SAS) AF: 0.268 AC: 811 AN: 3030

European-Finnish (FIN) AF: 0.107 AC: 2227 AN: 20824

Middle Eastern (MID) AF: 0.250 AC: 322 AN: 1290

European-Non Finnish (NFE) AF: 0.0941 AC: 14849 AN: 157784

Other (OTH) AF: 0.221 AC: 3613 AN: 16346

GnomAD4 genome AF: 0.329 AC: 50070 AN: 152086 Hom.: 15822 Cov.: 32 AF XY: 0.329 AC XY: 24465 AN XY: 74352

African (AFR) AF: 0.823 AC: 34111 AN: 41464

American (AMR) AF: 0.281 AC: 4300 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1932 AN: 5164

South Asian (SAS) AF: 0.280 AC: 1352 AN: 4828

European-Finnish (FIN) AF: 0.113 AC: 1202 AN: 10600

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.0875 AC: 5946 AN: 67970

Other (OTH) AF: 0.295 AC: 622 AN: 2106

Alfa AF: 0.184 Hom.: 18618

Bravo AF: 0.366

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.7
DANN	Benign	0.79
PhyloP100		0.16
Mutation Taster		=99/1	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7732591;

hg19: chr5-142125177;