rs2619536

Variant names:

• chr6-15663616-T-C
• rs2619536

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 0.148 in 152,096 control chromosomes in the GnomAD database, including 2,326 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 0.15 (2326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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: 0.148 AC: 22479 AN: 151978 Hom.: 2329 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0506

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.148 AC: 22489 AN: 152096 Hom.: 2326 Cov.: 32 AF XY: 0.144 AC XY: 10679 AN XY: 74360

African (AFR) AF: 0.292 AC: 12101 AN: 41440

American (AMR) AF: 0.155 AC: 2373 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5176

South Asian (SAS) AF: 0.0515 AC: 248 AN: 4820

European-Finnish (FIN) AF: 0.0704 AC: 747 AN: 10604

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6371 AN: 67994

Other (OTH) AF: 0.125 AC: 263 AN: 2110

Alfa AF: 0.115 Hom.: 1605

Bravo AF: 0.163

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2619536; hg19: chr6-15663847;