rs2535327

Variant names:

• chr6-30859127-T-C
• rs2535327

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 0.256 in 151,922 control chromosomes in the GnomAD database, including 6,130 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 0.26 (6130 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 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: 0.256 AC: 38899 AN: 151804 Hom.: 6134 Cov.: 31

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.256 AC: 38892 AN: 151922 Hom.: 6130 Cov.: 31 AF XY: 0.256 AC XY: 19012 AN XY: 74236

African (AFR) AF: 0.0783 AC: 3248 AN: 41462

American (AMR) AF: 0.228 AC: 3476 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1330 AN: 3462

East Asian (EAS) AF: 0.189 AC: 977 AN: 5174

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4804

European-Finnish (FIN) AF: 0.389 AC: 4099 AN: 10524

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23839 AN: 67932

Other (OTH) AF: 0.252 AC: 530 AN: 2102

Alfa AF: 0.305 Hom.: 15885

Bravo AF: 0.237

Asia WGS AF: 0.158 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.24
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2535327; hg19: chr6-30826904;