6-32996919-A-T

Variant names:

• chr6-32996919-A-T
• rs206765

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 0.342 in 151,868 control chromosomes in the GnomAD database, including 9,414 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 0.34 (9414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 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: 0.342 AC: 51951 AN: 151750 Hom.: 9413 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.342 AC: 51958 AN: 151868 Hom.: 9414 Cov.: 32 AF XY: 0.346 AC XY: 25707 AN XY: 74222

African (AFR) AF: 0.250 AC: 10354 AN: 41436

American (AMR) AF: 0.303 AC: 4632 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1872 AN: 5182

South Asian (SAS) AF: 0.373 AC: 1792 AN: 4806

European-Finnish (FIN) AF: 0.469 AC: 4932 AN: 10520

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25902 AN: 67860

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.374 Hom.: 6236

Bravo AF: 0.323

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.83
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs206765; hg19: chr6-32964696;