rs1701821

Variant names:

• chr7-113310616-G-A
• rs1701821

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 0.214 in 151,538 control chromosomes in the GnomAD database, including 3,709 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 0.21 (3709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 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: 0.214 AC: 32392 AN: 151420 Hom.: 3697 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.214 AC: 32450 AN: 151538 Hom.: 3709 Cov.: 32 AF XY: 0.220 AC XY: 16297 AN XY: 74036

African (AFR) AF: 0.260 AC: 10758 AN: 41390

American (AMR) AF: 0.196 AC: 2980 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 506 AN: 3452

East Asian (EAS) AF: 0.179 AC: 916 AN: 5124

South Asian (SAS) AF: 0.329 AC: 1587 AN: 4820

European-Finnish (FIN) AF: 0.281 AC: 2967 AN: 10558

Middle Eastern (MID) AF: 0.159 AC: 46 AN: 290

European-Non Finnish (NFE) AF: 0.181 AC: 12231 AN: 67708

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.184 Hom.: 431

Bravo AF: 0.208

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1701821; hg19: chr7-112950671;