chr6-120864924-G-A

Variant names:

• chr6-120864924-G-A
• rs2817955

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 151,298 control chromosomes in the GnomAD database, including 17,328 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 (17328 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.439 AC: 66398 AN: 151180 Hom.: 17280 Cov.: 31

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.440 AC: 66511 AN: 151298 Hom.: 17328 Cov.: 31 AF XY: 0.440 AC XY: 32562 AN XY: 73956

African (AFR) AF: 0.684 AC: 28318 AN: 41376

American (AMR) AF: 0.561 AC: 8512 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3460

East Asian (EAS) AF: 0.594 AC: 3059 AN: 5154

South Asian (SAS) AF: 0.527 AC: 2531 AN: 4804

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10560

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

European-Non Finnish (NFE) AF: 0.288 AC: 19429 AN: 67472

Other (OTH) AF: 0.436 AC: 910 AN: 2086

Alfa AF: 0.217 Hom.: 465

Bravo AF: 0.476

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.65
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2817955; hg19: chr6-121186070;