chr1-100809462-G-T

Variant names:

• chr1-100809462-G-T
• rs6673745

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 0.361 in 151,782 control chromosomes in the GnomAD database, including 10,648 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 0.36 (10648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.361 AC: 54761 AN: 151664 Hom.: 10647 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.361 AC: 54778 AN: 151782 Hom.: 10648 Cov.: 31 AF XY: 0.360 AC XY: 26698 AN XY: 74158

African (AFR) AF: 0.222 AC: 9196 AN: 41368

American (AMR) AF: 0.351 AC: 5353 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1554 AN: 5142

South Asian (SAS) AF: 0.476 AC: 2280 AN: 4792

European-Finnish (FIN) AF: 0.376 AC: 3958 AN: 10518

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29491 AN: 67932

Other (OTH) AF: 0.356 AC: 752 AN: 2112

Alfa AF: 0.382 Hom.: 1975

Bravo AF: 0.347

Asia WGS AF: 0.353 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.66
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6673745; hg19: chr1-101275018;