rs7670734

Variant names:

• chr4-169151432-T-A
• rs7670734
• NM_020870.4:c.765+4048A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-169151432-T-A
• chr4-169151432-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020870.4(SH3RF1):​c.765+4048A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,114 control chromosomes in the GnomAD database, including 8,117 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 0.32 (8117 hom., cov: 33)
• Consequence: SH3RF1 NM_020870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

SH3RF1 (HGNC:17650): (SH3 domain containing ring finger 1) This gene encodes a protein containing an N-terminus RING-finger, four SH3 domains, and a region implicated in binding of the Rho GTPase Rac. Via the RING-finger, the encoded protein has been shown to function as an ubiquitin-protein ligase involved in protein sorting at the trans-Golgi network. The encoded protein may also act as a scaffold for the c-Jun N-terminal kinase signaling pathway, facilitating the formation of a functional signaling module. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -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 = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3RF1	NM_020870.4	c.765+4048A>T		intron_variant	Intron 4 of 11	ENST00000284637.14	NP_065921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3RF1	ENST00000284637.14	c.765+4048A>T		intron_variant	Intron 4 of 11	1	NM_020870.4	ENSP00000284637.9
SH3RF1	ENST00000508685.1	n.646+4048A>T		intron_variant	Intron 3 of 8	1
SH3RF1	ENST00000511421.5	n.348+4048A>T		intron_variant	Intron 2 of 7	1		ENSP00000426418.1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48650 AN: 151998 Hom.: 8102 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.320 AC: 48701 AN: 152114 Hom.: 8117 Cov.: 33 AF XY: 0.317 AC XY: 23576 AN XY: 74380

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.287

Alfa AF: 0.190 Hom.: 391

Bravo AF: 0.317

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs7670734; hg19: chr4-170072583;