chr1-105401679-T-A

Variant names:

• chr1-105401679-T-A
• rs2048839

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 0.41 in 151,824 control chromosomes in the GnomAD database, including 13,462 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 0.41 (13462 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 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: 0.410 AC: 62241 AN: 151706 Hom.: 13458 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.410 AC: 62266 AN: 151824 Hom.: 13462 Cov.: 31 AF XY: 0.409 AC XY: 30320 AN XY: 74190

African (AFR) AF: 0.302 AC: 12504 AN: 41442

American (AMR) AF: 0.449 AC: 6848 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3470

East Asian (EAS) AF: 0.193 AC: 992 AN: 5144

South Asian (SAS) AF: 0.306 AC: 1476 AN: 4816

European-Finnish (FIN) AF: 0.516 AC: 5425 AN: 10510

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

European-Non Finnish (NFE) AF: 0.466 AC: 31658 AN: 67890

Other (OTH) AF: 0.404 AC: 852 AN: 2110

Alfa AF: 0.439 Hom.: 1868

Bravo AF: 0.401

Asia WGS AF: 0.261 AC: 910 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs2048839; hg19: chr1-105944301;