6-86152161-T-G

Variant names:

• chr6-86152161-T-G
• rs220420

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 0.65 in 152,060 control chromosomes in the GnomAD database, including 32,380 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 0.65 (32380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.650 AC: 98725 AN: 151942 Hom.: 32360 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.650 AC: 98792 AN: 152060 Hom.: 32380 Cov.: 32 AF XY: 0.652 AC XY: 48450 AN XY: 74312

African (AFR) AF: 0.674 AC: 27942 AN: 41466

American (AMR) AF: 0.652 AC: 9968 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1818 AN: 3466

East Asian (EAS) AF: 0.637 AC: 3274 AN: 5140

South Asian (SAS) AF: 0.514 AC: 2479 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8194 AN: 10594

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43238 AN: 67970

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.624 Hom.: 20704

Bravo AF: 0.660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.33
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs220420; hg19: chr6-86861879;