1-105414627-T-G

Variant names:

• chr1-105414627-T-G
• rs987243

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 0.434 in 151,842 control chromosomes in the GnomAD database, including 14,695 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 0.43 (14695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.434 AC: 65854 AN: 151724 Hom.: 14690 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.434 AC: 65882 AN: 151842 Hom.: 14695 Cov.: 32 AF XY: 0.432 AC XY: 32065 AN XY: 74192

African (AFR) AF: 0.388 AC: 16087 AN: 41452

American (AMR) AF: 0.454 AC: 6927 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1793 AN: 3468

East Asian (EAS) AF: 0.192 AC: 988 AN: 5158

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4808

European-Finnish (FIN) AF: 0.516 AC: 5427 AN: 10526

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31596 AN: 67862

Other (OTH) AF: 0.418 AC: 881 AN: 2106

Alfa AF: 0.449 Hom.: 15101

Bravo AF: 0.427

Asia WGS AF: 0.263 AC: 915 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs987243; hg19: chr1-105957249;