rs10464444

Variant names:

• chr7-141832387-G-A
• rs10464444

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 0.27 in 151,908 control chromosomes in the GnomAD database, including 5,983 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 0.27 (5983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40933 AN: 151790 Hom.: 5980 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.270 AC: 40950 AN: 151908 Hom.: 5983 Cov.: 32 AF XY: 0.272 AC XY: 20214 AN XY: 74244

African (AFR) AF: 0.157 AC: 6515 AN: 41448

American (AMR) AF: 0.338 AC: 5163 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2386 AN: 5170

South Asian (SAS) AF: 0.302 AC: 1453 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2929 AN: 10540

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20603 AN: 67878

Other (OTH) AF: 0.284 AC: 598 AN: 2108

Alfa AF: 0.293 Hom.: 14201

Bravo AF: 0.271

Asia WGS AF: 0.371 AC: 1285 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10464444; hg19: chr7-141532187;