rs3747767

Variant names:

• chr6-79547564-C-A
• rs3747767
• ENST00000718102.1:c.140+8721C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-79547564-C-A
• chr6-79547564-C-G

Variant summary

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

The ENST00000718102.1(SH3BGRL2):​c.140+8721C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 152,176 control chromosomes in the GnomAD database, including 1,422 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 0.090 (1422 hom., cov: 31)
• Consequence: SH3BGRL2 ENST00000718102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 5 publications found

Genes affected

SH3BGRL2 (HGNC:15567): (SH3 domain binding glutamate rich protein like 2) Predicted to enable SH3 domain binding activity. Located in nuclear membrane and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3BGRL2	NR_171675.1	n.368+8721C>A		intron_variant	Intron 2 of 4
SH3BGRL2	XM_047419390.1	c.140+8721C>A		intron_variant	Intron 2 of 3		XP_047275346.1
SH3BGRL2	XM_047419391.1	c.-5042+8721C>A		intron_variant	Intron 2 of 5		XP_047275347.1
SH3BGRL2	XM_047419392.1	c.-699+8721C>A		intron_variant	Intron 2 of 5		XP_047275348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3BGRL2	ENST00000718102.1	c.140+8721C>A		intron_variant	Intron 2 of 3			ENSP00000520671.1
SH3BGRL2	ENST00000718104.1	c.80+8721C>A		intron_variant	Intron 2 of 5			ENSP00000520672.1
SH3BGRL2	ENST00000607718.2	c.140+8721C>A		intron_variant	Intron 2 of 2	6		ENSP00000520676.1

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13591 AN: 152058 Hom.: 1414 Cov.: 31

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0678

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0895 AC: 13625 AN: 152176 Hom.: 1422 Cov.: 31 AF XY: 0.0963 AC XY: 7166 AN XY: 74402

African (AFR) AF: 0.0459 AC: 1909 AN: 41550

American (AMR) AF: 0.219 AC: 3346 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 235 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2810 AN: 5138

South Asian (SAS) AF: 0.176 AC: 845 AN: 4814

European-Finnish (FIN) AF: 0.0849 AC: 900 AN: 10604

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3248 AN: 68006

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.0682 Hom.: 1493

Bravo AF: 0.105

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.55
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3747767; hg19: chr6-80257281;