1-163895097-C-T

Variant names:

• chr1-163895097-C-T
• rs1441178

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 0.655 in 152,018 control chromosomes in the GnomAD database, including 32,987 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 0.65 (32987 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.655 AC: 99447 AN: 151900 Hom.: 32945 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.655 AC: 99542 AN: 152018 Hom.: 32987 Cov.: 31 AF XY: 0.655 AC XY: 48660 AN XY: 74304

African (AFR) AF: 0.716 AC: 29709 AN: 41470

American (AMR) AF: 0.645 AC: 9858 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3466

East Asian (EAS) AF: 0.393 AC: 2025 AN: 5152

South Asian (SAS) AF: 0.522 AC: 2513 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7494 AN: 10568

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43801 AN: 67960

Other (OTH) AF: 0.611 AC: 1289 AN: 2110

Alfa AF: 0.633 Hom.: 49575

Bravo AF: 0.649

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.30
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs1441178; hg19: chr1-163864334;