6-115457596-T-A

Variant names:

• chr6-115457596-T-A
• rs2032558

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 0.444 in 151,750 control chromosomes in the GnomAD database, including 15,048 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 0.44 (15048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 2 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 = 0.447 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: 0.444 AC: 67301 AN: 151632 Hom.: 15042 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.444 AC: 67342 AN: 151750 Hom.: 15048 Cov.: 32 AF XY: 0.447 AC XY: 33157 AN XY: 74156

African (AFR) AF: 0.453 AC: 18756 AN: 41436

American (AMR) AF: 0.421 AC: 6393 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2285 AN: 5154

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4820

European-Finnish (FIN) AF: 0.500 AC: 5271 AN: 10540

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

European-Non Finnish (NFE) AF: 0.435 AC: 29533 AN: 67830

Other (OTH) AF: 0.449 AC: 946 AN: 2106

Alfa AF: 0.278 Hom.: 647

Bravo AF: 0.436

Asia WGS AF: 0.393 AC: 1362 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.76
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs2032558; hg19: chr6-115778760;