7-50439980-C-T

Variant names:

• chr7-50439980-C-T
• rs963739

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0330 AC: 1368 AN: 41460

American (AMR) AF: 0.102 AC: 1560 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2220 AN: 5172

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4812

European-Finnish (FIN) AF: 0.152 AC: 1606 AN: 10556

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11962 AN: 67956

Other (OTH) AF: 0.133 AC: 281 AN: 2112

Alfa AF: 0.143 Hom.: 946

Bravo AF: 0.129

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.070
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs963739; hg19: chr7-50507678;