6-109895628-T-G

Variant names:

• chr6-109895628-T-G
• rs4245540

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 0.38 in 152,056 control chromosomes in the GnomAD database, including 11,791 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 0.38 (11791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.380 AC: 57784 AN: 151938 Hom.: 11784 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.380 AC: 57818 AN: 152056 Hom.: 11791 Cov.: 32 AF XY: 0.378 AC XY: 28065 AN XY: 74308

African (AFR) AF: 0.225 AC: 9349 AN: 41480

American (AMR) AF: 0.441 AC: 6746 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1910 AN: 5170

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3836 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30712 AN: 67972

Other (OTH) AF: 0.439 AC: 925 AN: 2106

Alfa AF: 0.308 Hom.: 1223

Bravo AF: 0.378

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.73
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4245540; hg19: chr6-110216831; COSMIC: COSV69419960;