1-105095799-C-T

Variant names:

• chr1-105095799-C-T
• rs11184419

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 0.594 in 151,942 control chromosomes in the GnomAD database, including 27,452 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 0.59 (27452 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.95
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.595 AC: 90274 AN: 151822 Hom.: 27444 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.594 AC: 90322 AN: 151942 Hom.: 27452 Cov.: 33 AF XY: 0.595 AC XY: 44168 AN XY: 74260

African (AFR) AF: 0.468 AC: 19364 AN: 41406

American (AMR) AF: 0.633 AC: 9667 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2185 AN: 3464

East Asian (EAS) AF: 0.678 AC: 3499 AN: 5164

South Asian (SAS) AF: 0.576 AC: 2782 AN: 4828

European-Finnish (FIN) AF: 0.614 AC: 6481 AN: 10552

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44236 AN: 67944

Other (OTH) AF: 0.599 AC: 1261 AN: 2106

Alfa AF: 0.631 Hom.: 21936

Bravo AF: 0.594

Asia WGS AF: 0.601 AC: 2085 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.19
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs11184419; hg19: chr1-105638421; COSMIC: COSV59984215;