1-91913286-T-C

Variant names:

• chr1-91913286-T-C
• rs2770186

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 0.538 in 151,860 control chromosomes in the GnomAD database, including 22,373 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 0.54 (22373 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 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: 0.538 AC: 81678 AN: 151742 Hom.: 22354 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.538 AC: 81734 AN: 151860 Hom.: 22373 Cov.: 31 AF XY: 0.533 AC XY: 39527 AN XY: 74178

African (AFR) AF: 0.496 AC: 20543 AN: 41424

American (AMR) AF: 0.456 AC: 6948 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1713 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2147 AN: 4798

European-Finnish (FIN) AF: 0.563 AC: 5917 AN: 10512

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40572 AN: 67952

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.572 Hom.: 78386

Bravo AF: 0.529

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2770186; hg19: chr1-92378843;