6-81036018-A-G

Variant names:

• chr6-81036018-A-G
• rs2120524

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.453 in 151,788 control chromosomes in the GnomAD database, including 16,390 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 0.45 (16390 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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: 0.452 AC: 68579 AN: 151670 Hom.: 16333 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.453 AC: 68699 AN: 151788 Hom.: 16390 Cov.: 31 AF XY: 0.455 AC XY: 33741 AN XY: 74178

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.445

Alfa AF: 0.386 Hom.: 21358

Bravo AF: 0.465

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2120524; hg19: chr6-81745735;