chr6-33015144-T-C

Variant names:

• chr6-33015144-T-C
• rs2395304

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 0.513 in 151,654 control chromosomes in the GnomAD database, including 20,365 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 0.51 (20365 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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: 0.513 AC: 77713 AN: 151536 Hom.: 20353 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.513 AC: 77759 AN: 151654 Hom.: 20365 Cov.: 33 AF XY: 0.516 AC XY: 38215 AN XY: 74068

African (AFR) AF: 0.626 AC: 25846 AN: 41292

American (AMR) AF: 0.443 AC: 6769 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1964 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2599 AN: 5158

South Asian (SAS) AF: 0.574 AC: 2768 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5530 AN: 10470

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30661 AN: 67868

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.476 Hom.: 40267

Bravo AF: 0.509

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2395304; hg19: chr6-32982921;