chr1-92506271-T-A

Position:

• chr1-92506271-T-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.836

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970705; hg19: chr1-92971828;