7-70892343-G-A

Variant names:

• chr7-70892343-G-A
• rs10248926

Variant summary

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

The variant allele was found at a frequency of 0.398 in 151,744 control chromosomes in the GnomAD database, including 13,101 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 0.40 (13101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60368 AN: 151626 Hom.: 13095 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.398 AC: 60390 AN: 151744 Hom.: 13101 Cov.: 31 AF XY: 0.405 AC XY: 30024 AN XY: 74114

African (AFR) AF: 0.225 AC: 9320 AN: 41396

American (AMR) AF: 0.437 AC: 6654 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2579 AN: 5110

South Asian (SAS) AF: 0.427 AC: 2050 AN: 4796

European-Finnish (FIN) AF: 0.613 AC: 6454 AN: 10532

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30697 AN: 67914

Other (OTH) AF: 0.404 AC: 851 AN: 2106

Alfa AF: 0.428 Hom.: 3721

Bravo AF: 0.382

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.57
DANN	Benign	0.80
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10248926; hg19: chr7-70357329;