chr7-139132494-T-G

Variant names:

• chr7-139132494-T-G
• rs7798474

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 0.399 in 152,054 control chromosomes in the GnomAD database, including 14,590 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 0.40 (14590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.399 AC: 60613 AN: 151936 Hom.: 14546 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.399 AC: 60718 AN: 152054 Hom.: 14590 Cov.: 32 AF XY: 0.407 AC XY: 30241 AN XY: 74362

African (AFR) AF: 0.643 AC: 26649 AN: 41444

American (AMR) AF: 0.406 AC: 6203 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.695 AC: 3595 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2131 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3641 AN: 10580

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16430 AN: 67954

Other (OTH) AF: 0.371 AC: 785 AN: 2114

Alfa AF: 0.292 Hom.: 32013

Bravo AF: 0.416

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.65
PromoterAI		0.0033	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7798474; hg19: chr7-138817240;