1-162067819-T-C

Variant names:

• chr1-162067819-T-C
• rs6659759

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 0.346 in 152,072 control chromosomes in the GnomAD database, including 9,532 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 0.35 (9532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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: 0.346 AC: 52557 AN: 151954 Hom.: 9532 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.346 AC: 52580 AN: 152072 Hom.: 9532 Cov.: 32 AF XY: 0.353 AC XY: 26236 AN XY: 74326

African (AFR) AF: 0.376 AC: 15574 AN: 41466

American (AMR) AF: 0.331 AC: 5055 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3470

East Asian (EAS) AF: 0.534 AC: 2765 AN: 5174

South Asian (SAS) AF: 0.636 AC: 3065 AN: 4820

European-Finnish (FIN) AF: 0.350 AC: 3698 AN: 10552

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20098 AN: 67988

Other (OTH) AF: 0.341 AC: 721 AN: 2114

Alfa AF: 0.340 Hom.: 1995

Bravo AF: 0.337

Asia WGS AF: 0.578 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs6659759; hg19: chr1-162037609;