6-67011595-T-C

Variant names:

• chr6-67011595-T-C
• rs12203791

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 0.895 in 152,106 control chromosomes in the GnomAD database, including 61,121 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 0.89 (61121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.966 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: 0.895 AC: 135972 AN: 151988 Hom.: 61061 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.895 AC: 136089 AN: 152106 Hom.: 61121 Cov.: 32 AF XY: 0.894 AC XY: 66490 AN XY: 74342

African (AFR) AF: 0.974 AC: 40476 AN: 41544

American (AMR) AF: 0.909 AC: 13851 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3118 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4446 AN: 5150

South Asian (SAS) AF: 0.847 AC: 4087 AN: 4824

European-Finnish (FIN) AF: 0.845 AC: 8947 AN: 10588

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58174 AN: 67972

Other (OTH) AF: 0.903 AC: 1908 AN: 2114

Alfa AF: 0.863 Hom.: 27796

Bravo AF: 0.902

Asia WGS AF: 0.876 AC: 3048 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12203791; hg19: chr6-67721488;