1-232110281-G-A

Variant names:

• chr1-232110281-G-A
• rs10746514

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 0.38 in 151,964 control chromosomes in the GnomAD database, including 11,434 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 0.38 (11434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.380 AC: 57769 AN: 151846 Hom.: 11419 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.380 AC: 57817 AN: 151964 Hom.: 11434 Cov.: 32 AF XY: 0.379 AC XY: 28162 AN XY: 74264

African (AFR) AF: 0.297 AC: 12288 AN: 41432

American (AMR) AF: 0.359 AC: 5493 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1298 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1824 AN: 4814

European-Finnish (FIN) AF: 0.446 AC: 4702 AN: 10542

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.432 AC: 29344 AN: 67946

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.414 Hom.: 29680

Bravo AF: 0.374

Asia WGS AF: 0.386 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs10746514; hg19: chr1-232246027;