1-211502423-T-C

Variant names:

• chr1-211502423-T-C
• rs11119752

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 0.466 in 152,008 control chromosomes in the GnomAD database, including 17,355 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 0.47 (17355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.607 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: 0.466 AC: 70757 AN: 151888 Hom.: 17332 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.466 AC: 70835 AN: 152008 Hom.: 17355 Cov.: 32 AF XY: 0.457 AC XY: 33971 AN XY: 74294

African (AFR) AF: 0.614 AC: 25430 AN: 41450

American (AMR) AF: 0.374 AC: 5723 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2178 AN: 5154

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4808

European-Finnish (FIN) AF: 0.326 AC: 3443 AN: 10558

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28996 AN: 67984

Other (OTH) AF: 0.462 AC: 973 AN: 2106

Alfa AF: 0.442 Hom.: 2661

Bravo AF: 0.473

Asia WGS AF: 0.458 AC: 1595 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	1.7
DANN	Benign	0.70
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs11119752; hg19: chr1-211675765;