7-44542387-T-C

Position:

• chr7-44542387-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44542387T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.199

Alfa AF: 0.186 Hom.: 4512

Bravo AF: 0.224

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17725246; hg19: chr7-44581986;