rs7528341

Variant names:

• chr1-36675573-C-T
• rs7528341

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 0.242 in 151,970 control chromosomes in the GnomAD database, including 4,886 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 0.24 (4886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 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: 0.242 AC: 36776 AN: 151852 Hom.: 4881 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.242 AC: 36813 AN: 151970 Hom.: 4886 Cov.: 32 AF XY: 0.240 AC XY: 17831 AN XY: 74288

African (AFR) AF: 0.355 AC: 14700 AN: 41406

American (AMR) AF: 0.174 AC: 2653 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 706 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5160

South Asian (SAS) AF: 0.147 AC: 706 AN: 4806

European-Finnish (FIN) AF: 0.212 AC: 2245 AN: 10584

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13601 AN: 67960

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.220 Hom.: 702

Bravo AF: 0.245

Asia WGS AF: 0.260 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.54
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs7528341; hg19: chr1-37141174;