rs6667243

Variant names:

• chr1-196972363-T-C
• rs6667243

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 0.623 in 151,856 control chromosomes in the GnomAD database, including 31,162 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 0.62 (31162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.623 AC: 94583 AN: 151738 Hom.: 31115 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.623 AC: 94681 AN: 151856 Hom.: 31162 Cov.: 32 AF XY: 0.630 AC XY: 46755 AN XY: 74242

African (AFR) AF: 0.811 AC: 33628 AN: 41458

American (AMR) AF: 0.671 AC: 10211 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2196 AN: 3466

East Asian (EAS) AF: 0.890 AC: 4611 AN: 5178

South Asian (SAS) AF: 0.672 AC: 3226 AN: 4802

European-Finnish (FIN) AF: 0.503 AC: 5308 AN: 10554

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33735 AN: 67872

Other (OTH) AF: 0.626 AC: 1320 AN: 2108

Alfa AF: 0.544 Hom.: 39302

Bravo AF: 0.645

Asia WGS AF: 0.767 AC: 2663 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.3
DANN	Benign	0.85
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6667243; hg19: chr1-196941493; COSMIC: COSV50455100;