chr1-165047762-A-G

Variant names:

• chr1-165047762-A-G
• rs986362

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 0.442 in 152,024 control chromosomes in the GnomAD database, including 15,288 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 0.44 (15288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 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: 0.442 AC: 67155 AN: 151904 Hom.: 15264 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.442 AC: 67224 AN: 152024 Hom.: 15288 Cov.: 32 AF XY: 0.448 AC XY: 33280 AN XY: 74302

African (AFR) AF: 0.452 AC: 18733 AN: 41478

American (AMR) AF: 0.581 AC: 8861 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1653 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2830 AN: 5158

South Asian (SAS) AF: 0.570 AC: 2748 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3980 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27035 AN: 67974

Other (OTH) AF: 0.456 AC: 960 AN: 2104

Alfa AF: 0.437 Hom.: 2545

Bravo AF: 0.458

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.44
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs986362; hg19: chr1-165016999;