chr6-120865573-T-G

Variant names:

• chr6-120865573-T-G
• rs2817954

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 0.44 in 151,514 control chromosomes in the GnomAD database, including 17,377 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 0.44 (17377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.440 AC: 66554 AN: 151396 Hom.: 17329 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.440 AC: 66666 AN: 151514 Hom.: 17377 Cov.: 33 AF XY: 0.441 AC XY: 32664 AN XY: 74100

African (AFR) AF: 0.684 AC: 28337 AN: 41426

American (AMR) AF: 0.561 AC: 8530 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3466

East Asian (EAS) AF: 0.603 AC: 3115 AN: 5166

South Asian (SAS) AF: 0.528 AC: 2549 AN: 4830

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10588

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19469 AN: 67538

Other (OTH) AF: 0.435 AC: 915 AN: 2102

Alfa AF: 0.378 Hom.: 1564

Bravo AF: 0.477

Asia WGS AF: 0.587 AC: 2035 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2817954; hg19: chr6-121186719; COSMIC: COSV60276054;