rs10754396

Variant names:

• chr1-119432630-G-A
• rs10754396

Your query was ambiguous. Multiple possible variants found:

• chr1-119432630-G-A
• chr1-119432630-G-C

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 0.259 in 151,736 control chromosomes in the GnomAD database, including 7,826 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 0.26 (7826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 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: 0.259 AC: 39220 AN: 151618 Hom.: 7805 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.259 AC: 39292 AN: 151736 Hom.: 7826 Cov.: 32 AF XY: 0.260 AC XY: 19248 AN XY: 74132

African (AFR) AF: 0.555 AC: 22918 AN: 41292

American (AMR) AF: 0.215 AC: 3285 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5166

South Asian (SAS) AF: 0.307 AC: 1472 AN: 4792

European-Finnish (FIN) AF: 0.0888 AC: 931 AN: 10480

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7757 AN: 67962

Other (OTH) AF: 0.246 AC: 521 AN: 2114

Alfa AF: 0.183 Hom.: 1703

Bravo AF: 0.279

Asia WGS AF: 0.298 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.53
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10754396; hg19: chr1-119975253;