2-38750470-A-G

Position:

• chr2-38750470-A-G

Variant summary

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

The NM_001031684.3(SRSF7):​c.29-276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,296 control chromosomes in the GnomAD database, including 38,425 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 0.71 (38425 hom., cov: 27)
• Consequence: SRSF7 NM_001031684.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

SRSF7 (HGNC:10789): (serine and arginine rich splicing factor 7) The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an N-terminal RNA recognition motif (RRM) for binding RNA and a C-terminal RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2018]

SRSF7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRSF7	NM_001031684.3	c.29-276T>C		intron_variant		ENST00000313117.11	NP_001026854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRSF7	ENST00000313117.11	c.29-276T>C		intron_variant		1	NM_001031684.3	ENSP00000325905.6

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107462 AN: 151184 Hom.: 38413 Cov.: 27

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.711 AC: 107517 AN: 151296 Hom.: 38425 Cov.: 27 AF XY: 0.713 AC XY: 52646 AN XY: 73882

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.733

Alfa AF: 0.700 Hom.: 29320

Bravo AF: 0.712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.51

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: rs3134628; hg19: chr2-38977612;