chr1-205499161-C-T

Variant names:

• chr1-205499161-C-T
• rs6681714

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 0.755 in 152,110 control chromosomes in the GnomAD database, including 44,114 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 0.76 (44114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.82 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: 0.755 AC: 114812 AN: 151992 Hom.: 44096 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.755 AC: 114874 AN: 152110 Hom.: 44114 Cov.: 31 AF XY: 0.753 AC XY: 55983 AN XY: 74362

African (AFR) AF: 0.655 AC: 27147 AN: 41474

American (AMR) AF: 0.619 AC: 9466 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2640 AN: 3472

East Asian (EAS) AF: 0.764 AC: 3945 AN: 5164

South Asian (SAS) AF: 0.827 AC: 3981 AN: 4812

European-Finnish (FIN) AF: 0.846 AC: 8967 AN: 10604

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56101 AN: 67980

Other (OTH) AF: 0.745 AC: 1571 AN: 2110

Alfa AF: 0.793 Hom.: 180104

Bravo AF: 0.727

Asia WGS AF: 0.798 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.20
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs6681714; hg19: chr1-205468289;