chr6-73899187-G-T

Variant names:

• chr6-73899187-G-T
• rs1529992

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 0.57 in 152,014 control chromosomes in the GnomAD database, including 26,051 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 0.57 (26051 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.570 AC: 86556 AN: 151894 Hom.: 26045 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.570 AC: 86593 AN: 152014 Hom.: 26051 Cov.: 33 AF XY: 0.572 AC XY: 42525 AN XY: 74334

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.598

Alfa AF: 0.622 Hom.: 13448

Bravo AF: 0.548

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529992; hg19: chr6-74608903; COSMIC: COSV69405165;