chr1-165372612-A-G

Variant names:

• chr1-165372612-A-G
• rs12081765

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 0.558 in 152,014 control chromosomes in the GnomAD database, including 23,971 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 0.56 (23971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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: 0.558 AC: 84779 AN: 151896 Hom.: 23954 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.558 AC: 84842 AN: 152014 Hom.: 23971 Cov.: 32 AF XY: 0.556 AC XY: 41321 AN XY: 74306

African (AFR) AF: 0.612 AC: 25379 AN: 41450

American (AMR) AF: 0.462 AC: 7064 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2221 AN: 5170

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4814

European-Finnish (FIN) AF: 0.624 AC: 6605 AN: 10580

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38072 AN: 67938

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.554 Hom.: 59588

Bravo AF: 0.551

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.35
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs12081765; hg19: chr1-165341849;