1-191193417-A-T

Variant names:

• chr1-191193417-A-T
• rs2061018

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 0.481 in 151,902 control chromosomes in the GnomAD database, including 17,685 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 0.48 (17685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.481 AC: 73017 AN: 151786 Hom.: 17671 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.481 AC: 73085 AN: 151902 Hom.: 17685 Cov.: 31 AF XY: 0.481 AC XY: 35709 AN XY: 74212

African (AFR) AF: 0.500 AC: 20732 AN: 41460

American (AMR) AF: 0.524 AC: 7983 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1817 AN: 3464

East Asian (EAS) AF: 0.372 AC: 1914 AN: 5146

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4856 AN: 10540

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32250 AN: 67916

Other (OTH) AF: 0.472 AC: 994 AN: 2108

Alfa AF: 0.367 Hom.: 988

Bravo AF: 0.485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2061018; hg19: chr1-191162547;