1-79805653-T-A

Position:

• chr1-79805653-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 0.645 in 152,028 control chromosomes in the GnomAD database, including 31,975 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 0.65 (31975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98057 AN: 151908 Hom.: 31955 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.645 AC: 98129 AN: 152028 Hom.: 31975 Cov.: 32 AF XY: 0.650 AC XY: 48321 AN XY: 74322

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.665

Alfa AF: 0.642 Hom.: 3958

Bravo AF: 0.648

Asia WGS AF: 0.668 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12037277; hg19: chr1-80271338;