rs10464444

Variant names:

• chr7-141832387-G-A
• rs10464444

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.270 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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.284

Alfa AF: 0.301 Hom.: 8168

Bravo AF: 0.271

Asia WGS AF: 0.371 AC: 1285 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10464444; hg19: chr7-141532187;