chr1-162066733-G-T

Variant names:

• chr1-162066733-G-T
• rs12567211

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 0.385 in 151,888 control chromosomes in the GnomAD database, including 12,280 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 0.39 (12280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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: 0.385 AC: 58461 AN: 151770 Hom.: 12266 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.385 AC: 58508 AN: 151888 Hom.: 12280 Cov.: 31 AF XY: 0.391 AC XY: 29022 AN XY: 74224

African (AFR) AF: 0.512 AC: 21188 AN: 41382

American (AMR) AF: 0.345 AC: 5278 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2750 AN: 5166

South Asian (SAS) AF: 0.636 AC: 3065 AN: 4818

European-Finnish (FIN) AF: 0.351 AC: 3697 AN: 10522

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20159 AN: 67930

Other (OTH) AF: 0.365 AC: 769 AN: 2106

Alfa AF: 0.351 Hom.: 3384

Bravo AF: 0.382

Asia WGS AF: 0.586 AC: 2034 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs12567211; hg19: chr1-162036523;