rs1701821

chr7-113310616-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.197

Alfa AF: 0.182 Hom.: 411

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1701821; hg19: chr7-112950671;