chr1-163530921-T-G

Variant names:

• chr1-163530921-T-G
• rs3001089

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 0.773 in 152,072 control chromosomes in the GnomAD database, including 49,393 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 0.77 (49393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 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: 0.774 AC: 117588 AN: 151952 Hom.: 49392 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.773 AC: 117620 AN: 152072 Hom.: 49393 Cov.: 32 AF XY: 0.780 AC XY: 57965 AN XY: 74334

African (AFR) AF: 0.410 AC: 16991 AN: 41442

American (AMR) AF: 0.871 AC: 13318 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3180 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4596 AN: 5152

South Asian (SAS) AF: 0.916 AC: 4418 AN: 4824

European-Finnish (FIN) AF: 0.939 AC: 9953 AN: 10598

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62359 AN: 67992

Other (OTH) AF: 0.806 AC: 1695 AN: 2102

Alfa AF: 0.834 Hom.: 12374

Bravo AF: 0.752

Asia WGS AF: 0.844 AC: 2932 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.88
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs3001089; hg19: chr1-163500711;