6-132573289-T-G

Variant names:

• chr6-132573289-T-G
• rs7745308

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 0.0624 in 152,178 control chromosomes in the GnomAD database, including 565 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 0.062 (565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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: 0.0624 AC: 9481 AN: 152060 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0624 AC: 9495 AN: 152178 Hom.: 565 Cov.: 32 AF XY: 0.0602 AC XY: 4482 AN XY: 74406

African (AFR) AF: 0.155 AC: 6420 AN: 41510

American (AMR) AF: 0.0418 AC: 639 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4820

European-Finnish (FIN) AF: 0.0143 AC: 151 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0280 AC: 1903 AN: 68000

Other (OTH) AF: 0.0678 AC: 143 AN: 2108

Alfa AF: 0.0730 Hom.: 297

Bravo AF: 0.0693

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.46
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs7745308; hg19: chr6-132894428;