rs375912

Variant names:

• chr6-33048951-T-C
• rs375912

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 0.274 in 152,098 control chromosomes in the GnomAD database, including 6,457 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 0.27 (6457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 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: 0.275 AC: 41736 AN: 151980 Hom.: 6452 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.274 AC: 41733 AN: 152098 Hom.: 6457 Cov.: 32 AF XY: 0.280 AC XY: 20798 AN XY: 74360

African (AFR) AF: 0.143 AC: 5949 AN: 41512

American (AMR) AF: 0.248 AC: 3788 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1602 AN: 5164

South Asian (SAS) AF: 0.483 AC: 2327 AN: 4820

European-Finnish (FIN) AF: 0.346 AC: 3655 AN: 10574

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21652 AN: 67966

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.306 Hom.: 27558

Bravo AF: 0.258

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.41
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs375912; hg19: chr6-33016728;