6-50992603-T-C

Variant names:

• chr6-50992603-T-C
• rs4715215

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 0.283 in 152,050 control chromosomes in the GnomAD database, including 6,537 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 0.28 (6537 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.338 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: 0.283 AC: 42978 AN: 151932 Hom.: 6540 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.283 AC: 42984 AN: 152050 Hom.: 6537 Cov.: 33 AF XY: 0.280 AC XY: 20797 AN XY: 74324

African (AFR) AF: 0.177 AC: 7366 AN: 41502

American (AMR) AF: 0.346 AC: 5270 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1131 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3018 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23024 AN: 67960

Other (OTH) AF: 0.262 AC: 552 AN: 2104

Alfa AF: 0.319 Hom.: 29863

Bravo AF: 0.283

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4715215; hg19: chr6-50960316;