rs4706387

Positions:

• chr6-91258867-A-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 0.32 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;