6-130789228-T-C

Variant names:

• chr6-130789228-T-C
• rs7741731

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 0.239 in 152,128 control chromosomes in the GnomAD database, including 5,133 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 0.24 (5133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.239 AC: 36323 AN: 152010 Hom.: 5129 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.239 AC: 36347 AN: 152128 Hom.: 5133 Cov.: 32 AF XY: 0.242 AC XY: 17992 AN XY: 74376

African (AFR) AF: 0.379 AC: 15748 AN: 41508

American (AMR) AF: 0.219 AC: 3341 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1520 AN: 5178

South Asian (SAS) AF: 0.277 AC: 1331 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10879 AN: 68000

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.179 Hom.: 4042

Bravo AF: 0.245

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.59
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7741731; hg19: chr6-131110370;