chr4-27478563-A-T

Variant names:

• chr4-27478563-A-T
• rs1947508

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 0.582 in 152,068 control chromosomes in the GnomAD database, including 26,026 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 0.58 (26026 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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: 0.582 AC: 88400 AN: 151950 Hom.: 25981 Cov.: 33

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.582 AC: 88506 AN: 152068 Hom.: 26026 Cov.: 33 AF XY: 0.579 AC XY: 43035 AN XY: 74298

African (AFR) AF: 0.661 AC: 27408 AN: 41484

American (AMR) AF: 0.603 AC: 9218 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1924 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2589 AN: 5180

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4822

European-Finnish (FIN) AF: 0.587 AC: 6202 AN: 10572

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37230 AN: 67948

Other (OTH) AF: 0.547 AC: 1154 AN: 2108

Alfa AF: 0.579 Hom.: 3030

Bravo AF: 0.590

Asia WGS AF: 0.461 AC: 1601 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1947508; hg19: chr4-27480185;