rs7074542

Variant names:

• chr10-122353283-C-T
• rs7074542

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 0.303 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.322 AC: 13364 AN: 41460

American (AMR) AF: 0.259 AC: 3956 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2081 AN: 5158

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2268 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20572 AN: 67964

Other (OTH) AF: 0.324 AC: 684 AN: 2112

Alfa AF: 0.292 Hom.: 974

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7074542; hg19: chr10-124112799;