7-25231077-T-G

Variant names:

• chr7-25231077-T-G
• rs7780038

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 0.198 in 152,068 control chromosomes in the GnomAD database, including 3,272 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 0.20 (3272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30145 AN: 151950 Hom.: 3274 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.198 AC: 30168 AN: 152068 Hom.: 3272 Cov.: 32 AF XY: 0.201 AC XY: 14959 AN XY: 74334

African (AFR) AF: 0.153 AC: 6361 AN: 41506

American (AMR) AF: 0.235 AC: 3584 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 626 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2586 AN: 5168

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4806

European-Finnish (FIN) AF: 0.226 AC: 2385 AN: 10562

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12727 AN: 67976

Other (OTH) AF: 0.211 AC: 447 AN: 2114

Alfa AF: 0.196 Hom.: 627

Bravo AF: 0.201

Asia WGS AF: 0.336 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.43
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7780038; hg19: chr7-25270696;