6-32687441-T-G

Variant names:

• chr6-32687441-T-G
• rs2856683

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 0.25 in 151,900 control chromosomes in the GnomAD database, including 5,089 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 0.25 (5089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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: 0.250 AC: 37993 AN: 151782 Hom.: 5084 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.250 AC: 38027 AN: 151900 Hom.: 5089 Cov.: 32 AF XY: 0.256 AC XY: 19027 AN XY: 74238

African (AFR) AF: 0.209 AC: 8660 AN: 41428

American (AMR) AF: 0.372 AC: 5677 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1175 AN: 3464

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5162

South Asian (SAS) AF: 0.344 AC: 1657 AN: 4812

European-Finnish (FIN) AF: 0.264 AC: 2773 AN: 10492

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15519 AN: 67956

Other (OTH) AF: 0.266 AC: 561 AN: 2110

Alfa AF: 0.311 Hom.: 6402

Bravo AF: 0.262

Asia WGS AF: 0.280 AC: 968 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.4
DANN	Benign	0.74
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2856683; hg19: chr6-32655218;