1-154697101-C-T

Variant names:

• chr1-154697101-C-T
• rs2036627

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 0.899 in 152,302 control chromosomes in the GnomAD database, including 61,616 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 0.90 (61616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.899 AC: 136817 AN: 152184 Hom.: 61581 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.899 AC: 136906 AN: 152302 Hom.: 61616 Cov.: 32 AF XY: 0.902 AC XY: 67151 AN XY: 74470

African (AFR) AF: 0.857 AC: 35589 AN: 41540

American (AMR) AF: 0.923 AC: 14117 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3205 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5051 AN: 5184

South Asian (SAS) AF: 0.950 AC: 4589 AN: 4832

European-Finnish (FIN) AF: 0.928 AC: 9854 AN: 10622

Middle Eastern (MID) AF: 0.932 AC: 272 AN: 292

European-Non Finnish (NFE) AF: 0.904 AC: 61499 AN: 68032

Other (OTH) AF: 0.905 AC: 1914 AN: 2114

Alfa AF: 0.901 Hom.: 16410

Bravo AF: 0.897

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.80
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2036627; hg19: chr1-154669577;