1-92500412-T-C

Variant names:

• chr1-92500412-T-C
• rs2031494

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 0.853 in 152,240 control chromosomes in the GnomAD database, including 55,750 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 0.85 (55750 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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: 0.853 AC: 129703 AN: 152122 Hom.: 55691 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.853 AC: 129824 AN: 152240 Hom.: 55750 Cov.: 32 AF XY: 0.855 AC XY: 63650 AN XY: 74440

African (AFR) AF: 0.930 AC: 38647 AN: 41558

American (AMR) AF: 0.869 AC: 13285 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3076 AN: 3466

East Asian (EAS) AF: 0.969 AC: 5030 AN: 5192

South Asian (SAS) AF: 0.952 AC: 4600 AN: 4834

European-Finnish (FIN) AF: 0.766 AC: 8106 AN: 10588

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54309 AN: 67996

Other (OTH) AF: 0.838 AC: 1773 AN: 2116

Alfa AF: 0.822 Hom.: 25877

Bravo AF: 0.861

Asia WGS AF: 0.956 AC: 3324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2031494; hg19: chr1-92965969;