chr6-55944249-T-A

Variant names:

• chr6-55944249-T-A
• rs4715571

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 0.526 in 151,676 control chromosomes in the GnomAD database, including 21,744 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 0.53 (21744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79655 AN: 151558 Hom.: 21707 Cov.: 31

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.526 AC: 79753 AN: 151676 Hom.: 21744 Cov.: 31 AF XY: 0.525 AC XY: 38935 AN XY: 74134

African (AFR) AF: 0.631 AC: 26140 AN: 41444

American (AMR) AF: 0.577 AC: 8791 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1827 AN: 3462

East Asian (EAS) AF: 0.167 AC: 862 AN: 5164

South Asian (SAS) AF: 0.371 AC: 1786 AN: 4808

European-Finnish (FIN) AF: 0.524 AC: 5534 AN: 10566

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 32949 AN: 67704

Other (OTH) AF: 0.531 AC: 1117 AN: 2104

Alfa AF: 0.334 Hom.: 783

Bravo AF: 0.534

Asia WGS AF: 0.326 AC: 1134 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.35
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4715571; hg19: chr6-55809047;