chr7-54462888-T-C

Variant names:

• chr7-54462888-T-C
• rs10499740

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 0.544 in 151,626 control chromosomes in the GnomAD database, including 23,329 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 0.54 (23329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.66 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: 0.544 AC: 82406 AN: 151508 Hom.: 23312 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.544 AC: 82471 AN: 151626 Hom.: 23329 Cov.: 32 AF XY: 0.546 AC XY: 40460 AN XY: 74106

African (AFR) AF: 0.373 AC: 15437 AN: 41366

American (AMR) AF: 0.641 AC: 9763 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2161 AN: 3464

East Asian (EAS) AF: 0.494 AC: 2543 AN: 5148

South Asian (SAS) AF: 0.680 AC: 3277 AN: 4822

European-Finnish (FIN) AF: 0.594 AC: 6238 AN: 10494

Middle Eastern (MID) AF: 0.510 AC: 148 AN: 290

European-Non Finnish (NFE) AF: 0.609 AC: 41283 AN: 67798

Other (OTH) AF: 0.549 AC: 1153 AN: 2100

Alfa AF: 0.580 Hom.: 4536

Bravo AF: 0.539

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.52
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10499740; hg19: chr7-54530581;