6-81283434-G-T

Variant names:

• chr6-81283434-G-T
• rs9361780

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 0.0527 in 151,662 control chromosomes in the GnomAD database, including 569 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 0.053 (569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.0527 AC: 7985 AN: 151544 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0324

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0466

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

GnomAD4 genome AF: 0.0527 AC: 8000 AN: 151662 Hom.: 569 Cov.: 32 AF XY: 0.0596 AC XY: 4418 AN XY: 74090

African (AFR) AF: 0.0103 AC: 427 AN: 41438

American (AMR) AF: 0.140 AC: 2123 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.0324 AC: 112 AN: 3458

East Asian (EAS) AF: 0.322 AC: 1654 AN: 5132

South Asian (SAS) AF: 0.166 AC: 798 AN: 4816

European-Finnish (FIN) AF: 0.0503 AC: 530 AN: 10538

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0331 AC: 2244 AN: 67822

Other (OTH) AF: 0.0485 AC: 102 AN: 2104

Alfa AF: 0.0399 Hom.: 345

Bravo AF: 0.0567

Asia WGS AF: 0.241 AC: 835 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9361780; hg19: chr6-81993151; COSMIC: COSV68670116;