6-86720747-T-G

Variant names:

• chr6-86720747-T-G
• rs1325182

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 0.395 in 151,992 control chromosomes in the GnomAD database, including 14,317 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 0.39 (14317 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.395 AC: 60014 AN: 151874 Hom.: 14313 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.395 AC: 60036 AN: 151992 Hom.: 14317 Cov.: 31 AF XY: 0.405 AC XY: 30062 AN XY: 74260

African (AFR) AF: 0.118 AC: 4910 AN: 41520

American (AMR) AF: 0.491 AC: 7494 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3325 AN: 5146

South Asian (SAS) AF: 0.461 AC: 2222 AN: 4820

European-Finnish (FIN) AF: 0.586 AC: 6166 AN: 10530

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33265 AN: 67942

Other (OTH) AF: 0.383 AC: 809 AN: 2110

Alfa AF: 0.447 Hom.: 12077

Bravo AF: 0.380

Asia WGS AF: 0.520 AC: 1805 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.87
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1325182; hg19: chr6-87430465;