7-15976238-G-C

Position:

• chr7-15976238-G-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 0.244 in 152,042 control chromosomes in the GnomAD database, including 5,382 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 (5382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37121 AN: 151924 Hom.: 5386 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0122

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.244 AC: 37113 AN: 152042 Hom.: 5382 Cov.: 32 AF XY: 0.241 AC XY: 17876 AN XY: 74306

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.273

Alfa AF: 0.287 Hom.: 849

Bravo AF: 0.233

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2052028; hg19: chr7-16015863;