1-214781596-T-C

Variant names:

• chr1-214781596-T-C
• rs6695352

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 0.528 in 151,862 control chromosomes in the GnomAD database, including 21,796 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 0.53 (21796 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80172 AN: 151742 Hom.: 21772 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.528 AC: 80251 AN: 151862 Hom.: 21796 Cov.: 31 AF XY: 0.541 AC XY: 40096 AN XY: 74170

African (AFR) AF: 0.584 AC: 24190 AN: 41404

American (AMR) AF: 0.563 AC: 8599 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1390 AN: 3462

East Asian (EAS) AF: 0.792 AC: 4088 AN: 5160

South Asian (SAS) AF: 0.639 AC: 3075 AN: 4814

European-Finnish (FIN) AF: 0.604 AC: 6353 AN: 10520

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30979 AN: 67916

Other (OTH) AF: 0.496 AC: 1045 AN: 2108

Alfa AF: 0.497 Hom.: 3056

Bravo AF: 0.526

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.20
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6695352; hg19: chr1-214954939;