6-89242511-G-T

Position:

• chr6-89242511-G-T

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 0.783 in 152,144 control chromosomes in the GnomAD database, including 47,247 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 0.78 (47247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119105 AN: 152026 Hom.: 47215 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.783 AC: 119190 AN: 152144 Hom.: 47247 Cov.: 32 AF XY: 0.785 AC XY: 58355 AN XY: 74382

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.759

Alfa AF: 0.748 Hom.: 19538

Bravo AF: 0.780

Asia WGS AF: 0.754 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.059
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282135; hg19: chr6-89952230;