7-127433905-T-C

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 0.321 in 152,018 control chromosomes in the GnomAD database, including 10,157 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 0.32 (10157 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48789 AN: 151900 Hom.: 10145 Cov.: 31

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.321 AC: 48808 AN: 152018 Hom.: 10157 Cov.: 31 AF XY: 0.331 AC XY: 24592 AN XY: 74268

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.319

Alfa AF: 0.358 Hom.: 1799

Bravo AF: 0.308

Asia WGS AF: 0.568 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.34
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487482; hg19: chr7-127073959;