7-50409515-T-C

Position:

• chr7-50409515-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 0.239 in 151,760 control chromosomes in the GnomAD database, including 4,597 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 (4597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.239 AC: 36296 AN: 151642 Hom.: 4594 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.239 AC: 36316 AN: 151760 Hom.: 4597 Cov.: 32 AF XY: 0.243 AC XY: 18034 AN XY: 74170

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.243

Alfa AF: 0.258 Hom.: 2549

Bravo AF: 0.231

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10272724; hg19: chr7-50477213;