6-135111414-T-C

Variant names:

• chr6-135111414-T-C
• rs9494145

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 0.186 in 145,888 control chromosomes in the GnomAD database, including 2,911 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 0.19 (2911 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 57 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 27076 AN: 145798 Hom.: 2910 Cov.: 30

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.0896

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.186 AC: 27085 AN: 145888 Hom.: 2911 Cov.: 30 AF XY: 0.187 AC XY: 13256 AN XY: 70916

African (AFR) AF: 0.0767 AC: 3004 AN: 39142

American (AMR) AF: 0.177 AC: 2580 AN: 14550

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 694 AN: 3420

East Asian (EAS) AF: 0.254 AC: 1280 AN: 5038

South Asian (SAS) AF: 0.100 AC: 459 AN: 4576

European-Finnish (FIN) AF: 0.324 AC: 3020 AN: 9314

Middle Eastern (MID) AF: 0.189 AC: 53 AN: 280

European-Non Finnish (NFE) AF: 0.234 AC: 15600 AN: 66678

Other (OTH) AF: 0.157 AC: 316 AN: 2008

Alfa AF: 0.214 Hom.: 16036

Bravo AF: 0.169

Asia WGS AF: 0.146 AC: 504 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.34
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9494145; hg19: chr6-135432552; COSMIC: COSV60283457;