1-67682670-T-C

Variant names:

• chr1-67682670-T-C
• rs520820

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 0.68 in 151,990 control chromosomes in the GnomAD database, including 36,799 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 0.68 (36799 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103371 AN: 151872 Hom.: 36804 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.680 AC: 103405 AN: 151990 Hom.: 36799 Cov.: 32 AF XY: 0.678 AC XY: 50352 AN XY: 74314

African (AFR) AF: 0.462 AC: 19143 AN: 41396

American (AMR) AF: 0.732 AC: 11179 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2683 AN: 3468

East Asian (EAS) AF: 0.526 AC: 2721 AN: 5174

South Asian (SAS) AF: 0.727 AC: 3503 AN: 4818

European-Finnish (FIN) AF: 0.774 AC: 8156 AN: 10538

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53546 AN: 68012

Other (OTH) AF: 0.708 AC: 1490 AN: 2106

Alfa AF: 0.750 Hom.: 23215

Bravo AF: 0.667

Asia WGS AF: 0.614 AC: 2136 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.76
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs520820; hg19: chr1-68148353;