7-50439980-C-T

Variant names:

• chr7-50439980-C-T
• rs963739

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 0.139 in 152,024 control chromosomes in the GnomAD database, including 2,056 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 0.14 (2056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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: 0.139 AC: 21143 AN: 151906 Hom.: 2056 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.139 AC: 21137 AN: 152024 Hom.: 2056 Cov.: 32 AF XY: 0.141 AC XY: 10463 AN XY: 74312

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.133

Alfa AF: 0.156 Hom.: 357

Bravo AF: 0.129

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.070
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963739; hg19: chr7-50507678;