rs7074542

chr10-122353283-C-T

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 0.303 in 152,058 control chromosomes in the GnomAD database, including 7,141 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 0.30 (7141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46103 AN: 151940 Hom.: 7138 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.303 AC: 46113 AN: 152058 Hom.: 7141 Cov.: 32 AF XY: 0.300 AC XY: 22324 AN XY: 74364

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.324

Alfa AF: 0.290 Hom.: 928

Bravo AF: 0.309

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
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: rs7074542; hg19: chr10-124112799;