rs6934027

chr6-11900673-G-Achr6-11900673-G-Cchr6-11900673-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 0.897 in 150,706 control chromosomes in the GnomAD database, including 61,161 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 0.90 (61161 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 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: 0.898 AC: 135169 AN: 150596 Hom.: 61121 Cov.: 27

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.897 AC: 135253 AN: 150706 Hom.: 61161 Cov.: 27 AF XY: 0.891 AC XY: 65512 AN XY: 73492

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.891

Alfa AF: 0.892 Hom.: 5638

Bravo AF: 0.894

Asia WGS AF: 0.669 AC: 2326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.42
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6934027; hg19: chr6-11900906; COSMIC: COSV66714651;