rs1294094

chr6-154009670-T-Achr6-154009670-T-C

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 0.487 in 151,856 control chromosomes in the GnomAD database, including 18,406 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 0.49 (18406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.487 AC: 73960 AN: 151738 Hom.: 18396 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.487 AC: 74009 AN: 151856 Hom.: 18406 Cov.: 32 AF XY: 0.497 AC XY: 36841 AN XY: 74200

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.501

Alfa AF: 0.357 Hom.: 976

Bravo AF: 0.484

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.26
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1294094; hg19: chr6-154330805; COSMIC: COSV70429518;