rs7791070

Variant names:

• chr7-17361403-T-C
• rs7791070
• ENST00000637807.1:c.2373+21175T>C

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+21175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,096 control chromosomes in the GnomAD database, including 8,943 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 0.31 (8943 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

ENSG00000283321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.2373+21175T>C		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47758 AN: 151978 Hom.: 8903 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47855 AN: 152096 Hom.: 8943 Cov.: 32 AF XY: 0.313 AC XY: 23287 AN XY: 74344

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.291

Alfa AF: 0.243 Hom.: 2359

Bravo AF: 0.339

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7791070; hg19: chr7-17401027;