7-25231077-T-G

Variant names:

• chr7-25231077-T-G
• rs7780038

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.211

Alfa AF: 0.197 Hom.: 613

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780038; hg19: chr7-25270696;