rs1294094

Variant names:

• chr6-154009670-T-A
• rs1294094

Your query was ambiguous. Multiple possible variants found:

• chr6-154009670-T-A
• chr6-154009670-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;