1-101461927-T-G

Variant names:

• chr1-101461927-T-G
• rs9324334

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 0.106 in 152,272 control chromosomes in the GnomAD database, including 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 0.11 (987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.106 AC: 16141 AN: 152154 Hom.: 982 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.106 AC: 16168 AN: 152272 Hom.: 987 Cov.: 33 AF XY: 0.107 AC XY: 7945 AN XY: 74456

African (AFR) AF: 0.140 AC: 5816 AN: 41556

American (AMR) AF: 0.0876 AC: 1341 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1308 AN: 5182

South Asian (SAS) AF: 0.140 AC: 676 AN: 4830

European-Finnish (FIN) AF: 0.0416 AC: 442 AN: 10618

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5780 AN: 67992

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.102 Hom.: 313

Bravo AF: 0.110

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.73
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs9324334; hg19: chr1-101927483;