1-224351238-C-T

Variant names:

• chr1-224351238-C-T
• rs11579964

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 0.115 in 148,020 control chromosomes in the GnomAD database, including 1,217 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 0.11 (1217 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.115 AC: 16975 AN: 147990 Hom.: 1218 Cov.: 31

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.000788

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.115 AC: 16968 AN: 148020 Hom.: 1217 Cov.: 31 AF XY: 0.110 AC XY: 7918 AN XY: 71844

African (AFR) AF: 0.0432 AC: 1740 AN: 40286

American (AMR) AF: 0.118 AC: 1747 AN: 14826

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 564 AN: 3448

East Asian (EAS) AF: 0.000790 AC: 4 AN: 5062

South Asian (SAS) AF: 0.0645 AC: 300 AN: 4650

European-Finnish (FIN) AF: 0.140 AC: 1267 AN: 9082

Middle Eastern (MID) AF: 0.221 AC: 62 AN: 280

European-Non Finnish (NFE) AF: 0.161 AC: 10866 AN: 67434

Other (OTH) AF: 0.129 AC: 263 AN: 2042

Alfa AF: 0.142 Hom.: 5466

Bravo AF: 0.110

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.22
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11579964; hg19: chr1-224538940; COSMIC: COSV60033901;