1-199994494-T-C

Variant names:

• chr1-199994494-T-C
• rs4465241

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 0.841 in 152,144 control chromosomes in the GnomAD database, including 53,947 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 0.84 (53947 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.841 AC: 127841 AN: 152026 Hom.: 53913 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.841 AC: 127928 AN: 152144 Hom.: 53947 Cov.: 32 AF XY: 0.846 AC XY: 62874 AN XY: 74362

African (AFR) AF: 0.802 AC: 33285 AN: 41502

American (AMR) AF: 0.887 AC: 13529 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3067 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5105 AN: 5180

South Asian (SAS) AF: 0.932 AC: 4489 AN: 4816

European-Finnish (FIN) AF: 0.843 AC: 8928 AN: 10592

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56702 AN: 68012

Other (OTH) AF: 0.845 AC: 1787 AN: 2114

Alfa AF: 0.841 Hom.: 168019

Bravo AF: 0.845

Asia WGS AF: 0.940 AC: 3268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.057
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4465241; hg19: chr1-199963622;