7-123391378-T-C

Variant names:

• chr7-123391378-T-C
• rs991980

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 0.603 in 151,968 control chromosomes in the GnomAD database, including 28,162 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 0.60 (28162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91530 AN: 151852 Hom.: 28125 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.603 AC: 91612 AN: 151968 Hom.: 28162 Cov.: 32 AF XY: 0.602 AC XY: 44742 AN XY: 74268

African (AFR) AF: 0.725 AC: 30067 AN: 41472

American (AMR) AF: 0.529 AC: 8074 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3470

East Asian (EAS) AF: 0.465 AC: 2401 AN: 5168

South Asian (SAS) AF: 0.736 AC: 3547 AN: 4822

European-Finnish (FIN) AF: 0.529 AC: 5578 AN: 10550

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38028 AN: 67908

Other (OTH) AF: 0.591 AC: 1246 AN: 2108

Alfa AF: 0.574 Hom.: 10652

Bravo AF: 0.602

Asia WGS AF: 0.607 AC: 2099 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs991980; hg19: chr7-123031432;