rs10486744

Variant names:

• chr7-42854955-C-G
• rs10486744

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 0.0464 in 152,160 control chromosomes in the GnomAD database, including 200 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 0.046 (200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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: 0.0464 AC: 7054 AN: 152042 Hom.: 198 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.0289

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0464 AC: 7058 AN: 152160 Hom.: 200 Cov.: 32 AF XY: 0.0474 AC XY: 3527 AN XY: 74388

African (AFR) AF: 0.0458 AC: 1900 AN: 41500

American (AMR) AF: 0.0441 AC: 674 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5178

South Asian (SAS) AF: 0.121 AC: 584 AN: 4808

European-Finnish (FIN) AF: 0.0350 AC: 371 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0466 AC: 3167 AN: 68010

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0447 Hom.: 24

Bravo AF: 0.0458

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.35
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs10486744; hg19: chr7-42894554;