7-44542387-T-C

Variant names:

• chr7-44542387-T-C
• rs17725246

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 0.23 in 151,870 control chromosomes in the GnomAD database, including 4,273 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 0.23 (4273 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 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: 0.230 AC: 34920 AN: 151752 Hom.: 4250 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.230 AC: 34993 AN: 151870 Hom.: 4273 Cov.: 32 AF XY: 0.238 AC XY: 17676 AN XY: 74226

African (AFR) AF: 0.246 AC: 10189 AN: 41438

American (AMR) AF: 0.244 AC: 3734 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 726 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1948 AN: 5134

South Asian (SAS) AF: 0.199 AC: 956 AN: 4812

European-Finnish (FIN) AF: 0.348 AC: 3665 AN: 10518

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13185 AN: 67912

Other (OTH) AF: 0.199 AC: 422 AN: 2116

Alfa AF: 0.195 Hom.: 8277

Bravo AF: 0.224

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.52
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs17725246; hg19: chr7-44581986;