7-23898387-C-T

Variant names:

• chr7-23898387-C-T
• rs1074548

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 0.593 in 151,480 control chromosomes in the GnomAD database, including 27,959 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 0.59 (27959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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: 0.593 AC: 89718 AN: 151358 Hom.: 27914 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.593 AC: 89822 AN: 151480 Hom.: 27959 Cov.: 32 AF XY: 0.591 AC XY: 43677 AN XY: 73926

African (AFR) AF: 0.771 AC: 31928 AN: 41434

American (AMR) AF: 0.604 AC: 9200 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4270 AN: 5176

South Asian (SAS) AF: 0.593 AC: 2844 AN: 4794

European-Finnish (FIN) AF: 0.424 AC: 4357 AN: 10274

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34073 AN: 67792

Other (OTH) AF: 0.539 AC: 1135 AN: 2106

Alfa AF: 0.537 Hom.: 2692

Bravo AF: 0.613

Asia WGS AF: 0.671 AC: 2324 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.46
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1074548; hg19: chr7-23938006; COSMIC: COSV69829541;