chr6-121452853-T-C

Variant names:

• chr6-121452853-T-C
• rs2389541

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 0.43 in 151,870 control chromosomes in the GnomAD database, including 16,900 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 0.43 (16900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.430 AC: 65257 AN: 151752 Hom.: 16866 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.430 AC: 65341 AN: 151870 Hom.: 16900 Cov.: 31 AF XY: 0.429 AC XY: 31835 AN XY: 74230

African (AFR) AF: 0.736 AC: 30468 AN: 41396

American (AMR) AF: 0.296 AC: 4519 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 903 AN: 3462

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5172

South Asian (SAS) AF: 0.258 AC: 1241 AN: 4816

European-Finnish (FIN) AF: 0.391 AC: 4115 AN: 10512

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21618 AN: 67960

Other (OTH) AF: 0.393 AC: 828 AN: 2106

Alfa AF: 0.344 Hom.: 31606

Bravo AF: 0.435

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.50
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2389541; hg19: chr6-121773999;