1-74833098-T-C

Variant names:

• chr1-74833098-T-C
• rs11161851

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 0.377 in 151,710 control chromosomes in the GnomAD database, including 12,018 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 0.38 (12018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.377 AC: 57118 AN: 151592 Hom.: 12011 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.377 AC: 57140 AN: 151710 Hom.: 12018 Cov.: 32 AF XY: 0.386 AC XY: 28588 AN XY: 74092

African (AFR) AF: 0.199 AC: 8263 AN: 41448

American (AMR) AF: 0.438 AC: 6662 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3468

East Asian (EAS) AF: 0.762 AC: 3899 AN: 5116

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4812

European-Finnish (FIN) AF: 0.506 AC: 5337 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 27985 AN: 67790

Other (OTH) AF: 0.422 AC: 888 AN: 2106

Alfa AF: 0.403 Hom.: 37172

Bravo AF: 0.365

Asia WGS AF: 0.557 AC: 1931 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs11161851; hg19: chr1-75298782;