7-16021383-T-C

Variant names:

• chr7-16021383-T-C
• rs7789550

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 0.509 in 151,826 control chromosomes in the GnomAD database, including 20,102 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 0.51 (20102 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.509 AC: 77201 AN: 151706 Hom.: 20087 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.509 AC: 77257 AN: 151826 Hom.: 20102 Cov.: 30 AF XY: 0.502 AC XY: 37220 AN XY: 74212

African (AFR) AF: 0.502 AC: 20755 AN: 41382

American (AMR) AF: 0.476 AC: 7251 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2270 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1189 AN: 5158

South Asian (SAS) AF: 0.377 AC: 1811 AN: 4808

European-Finnish (FIN) AF: 0.454 AC: 4779 AN: 10536

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.548 AC: 37254 AN: 67922

Other (OTH) AF: 0.554 AC: 1167 AN: 2106

Alfa AF: 0.516 Hom.: 7964

Bravo AF: 0.514

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.71
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs7789550; hg19: chr7-16061008;