rs500456

Variant names:

• chr7-54531089-A-G
• rs500456

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 0.463 in 152,066 control chromosomes in the GnomAD database, including 16,981 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 0.46 (16981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.462 AC: 70268 AN: 151946 Hom.: 16939 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.463 AC: 70373 AN: 152066 Hom.: 16981 Cov.: 32 AF XY: 0.462 AC XY: 34351 AN XY: 74328

African (AFR) AF: 0.595 AC: 24666 AN: 41476

American (AMR) AF: 0.473 AC: 7220 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1740 AN: 5180

South Asian (SAS) AF: 0.351 AC: 1695 AN: 4828

European-Finnish (FIN) AF: 0.428 AC: 4522 AN: 10568

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27936 AN: 67960

Other (OTH) AF: 0.425 AC: 895 AN: 2106

Alfa AF: 0.428 Hom.: 2905

Bravo AF: 0.473

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.23
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs500456; hg19: chr7-54598782;