rs56279505

Variant names:

• chr4-99374083-T-A
• rs56279505

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 0.0952 in 152,208 control chromosomes in the GnomAD database, including 777 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 0.095 (777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0952 AC: 14480 AN: 152090 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0952 AC: 14496 AN: 152208 Hom.: 777 Cov.: 32 AF XY: 0.0978 AC XY: 7279 AN XY: 74420

African (AFR) AF: 0.0559 AC: 2324 AN: 41542

American (AMR) AF: 0.102 AC: 1560 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3470

East Asian (EAS) AF: 0.141 AC: 731 AN: 5176

South Asian (SAS) AF: 0.0961 AC: 464 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1666 AN: 10582

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.109 AC: 7400 AN: 68006

Other (OTH) AF: 0.0865 AC: 183 AN: 2116

Alfa AF: 0.104 Hom.: 113

Bravo AF: 0.0901

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.94
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs56279505; hg19: chr4-100295240; COSMIC: COSV107199798;