rs6914006

Variant names:

• chr6-89248042-A-G
• rs6914006

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.576 in 152,074 control chromosomes in the GnomAD database, including 26,850 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 0.58 (26850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87550 AN: 151956 Hom.: 26822 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.576 AC: 87620 AN: 152074 Hom.: 26850 Cov.: 32 AF XY: 0.567 AC XY: 42114 AN XY: 74338

African (AFR) AF: 0.744 AC: 30864 AN: 41496

American (AMR) AF: 0.391 AC: 5972 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3472

East Asian (EAS) AF: 0.0879 AC: 455 AN: 5178

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4820

European-Finnish (FIN) AF: 0.543 AC: 5730 AN: 10550

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38916 AN: 67964

Other (OTH) AF: 0.547 AC: 1155 AN: 2110

Alfa AF: 0.574 Hom.: 24342

Bravo AF: 0.570

Asia WGS AF: 0.341 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.23
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6914006; hg19: chr6-89957761;