chr6-91258867-A-T

Variant names:

• chr6-91258867-A-T
• rs4706387

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 0.32 in 152,050 control chromosomes in the GnomAD database, including 8,510 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 0.32 (8510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.320 AC: 48641 AN: 151932 Hom.: 8480 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.320 AC: 48717 AN: 152050 Hom.: 8510 Cov.: 32 AF XY: 0.325 AC XY: 24176 AN XY: 74318

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.296

Alfa AF: 0.293 Hom.: 883

Bravo AF: 0.327

Asia WGS AF: 0.518 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4706387; hg19: chr6-91968585; COSMIC: COSV69412946;