rs7754521

Variant names:

• chr6-153605318-C-T
• rs7754521

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 0.244 in 152,092 control chromosomes in the GnomAD database, including 6,098 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 (6098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.244 AC: 37031 AN: 151974 Hom.: 6093 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.244 AC: 37059 AN: 152092 Hom.: 6098 Cov.: 32 AF XY: 0.237 AC XY: 17613 AN XY: 74342

African (AFR) AF: 0.469 AC: 19422 AN: 41448

American (AMR) AF: 0.186 AC: 2835 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5184

South Asian (SAS) AF: 0.121 AC: 586 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10608

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11347 AN: 67982

Other (OTH) AF: 0.237 AC: 500 AN: 2108

Alfa AF: 0.196 Hom.: 11020

Bravo AF: 0.258

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.46
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7754521; hg19: chr6-153926453; COSMIC: COSV60293705;