6-79547564-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000718102.1(SH3BGRL2):​c.140+8721C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3BGRL2	NR_171675.1	n.368+8721C>G		intron_variant	Intron 2 of 4
SH3BGRL2	XM_047419390.1	c.140+8721C>G		intron_variant	Intron 2 of 3		XP_047275346.1
SH3BGRL2	XM_047419391.1	c.-5042+8721C>G		intron_variant	Intron 2 of 5		XP_047275347.1
SH3BGRL2	XM_047419392.1	c.-699+8721C>G		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>G		intron_variant	Intron 2 of 3			ENSP00000520671.1
SH3BGRL2	ENST00000718104.1	c.80+8721C>G		intron_variant	Intron 2 of 5			ENSP00000520672.1
SH3BGRL2	ENST00000607718.2	c.140+8721C>G		intron_variant	Intron 2 of 2	6		ENSP00000520676.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.43
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;