chr1-92506271-T-A

Variant names:

• chr1-92506271-T-A
• rs4970705

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 0.852 in 152,146 control chromosomes in the GnomAD database, including 55,665 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 (55665 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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: 0.852 AC: 129574 AN: 152028 Hom.: 55608 Cov.: 31

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.852 AC: 129693 AN: 152146 Hom.: 55665 Cov.: 31 AF XY: 0.855 AC XY: 63572 AN XY: 74378

African (AFR) AF: 0.929 AC: 38574 AN: 41512

American (AMR) AF: 0.869 AC: 13286 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3081 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5014 AN: 5178

South Asian (SAS) AF: 0.952 AC: 4589 AN: 4820

European-Finnish (FIN) AF: 0.766 AC: 8088 AN: 10564

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

European-Non Finnish (NFE) AF: 0.799 AC: 54293 AN: 67990

Other (OTH) AF: 0.836 AC: 1770 AN: 2116

Alfa AF: 0.837 Hom.: 6665

Bravo AF: 0.861

Asia WGS AF: 0.955 AC: 3320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4970705; hg19: chr1-92971828;