rs7542594

Variant names:

• chr1-36128255-T-C
• rs7542594

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 0.612 in 152,006 control chromosomes in the GnomAD database, including 30,608 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 0.61 (30608 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 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: 0.612 AC: 93002 AN: 151888 Hom.: 30604 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.612 AC: 93029 AN: 152006 Hom.: 30608 Cov.: 31 AF XY: 0.605 AC XY: 44915 AN XY: 74280

African (AFR) AF: 0.385 AC: 15954 AN: 41446

American (AMR) AF: 0.605 AC: 9244 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2323 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2134 AN: 5162

South Asian (SAS) AF: 0.574 AC: 2762 AN: 4810

European-Finnish (FIN) AF: 0.647 AC: 6843 AN: 10572

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51639 AN: 67960

Other (OTH) AF: 0.629 AC: 1325 AN: 2106

Alfa AF: 0.694 Hom.: 13605

Bravo AF: 0.596

Asia WGS AF: 0.528 AC: 1838 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	8.1
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7542594; hg19: chr1-36593856; COSMIC: COSV67295490;