1-163536287-T-G

Variant names:

• chr1-163536287-T-G
• rs1934496

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 0.305 in 152,056 control chromosomes in the GnomAD database, including 7,355 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 0.31 (7355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.305 AC: 46402 AN: 151938 Hom.: 7352 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.305 AC: 46426 AN: 152056 Hom.: 7355 Cov.: 32 AF XY: 0.306 AC XY: 22729 AN XY: 74316

African (AFR) AF: 0.221 AC: 9157 AN: 41490

American (AMR) AF: 0.310 AC: 4734 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1911 AN: 5152

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3352 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23834 AN: 67972

Other (OTH) AF: 0.318 AC: 671 AN: 2112

Alfa AF: 0.327 Hom.: 16692

Bravo AF: 0.297

Asia WGS AF: 0.360 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1934496; hg19: chr1-163506077;