6-93201401-T-C

Variant names:

• chr6-93201401-T-C
• rs12527818

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 0.243 in 151,878 control chromosomes in the GnomAD database, including 5,333 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 0.24 (5333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.243 AC: 36843 AN: 151762 Hom.: 5329 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.243 AC: 36871 AN: 151878 Hom.: 5333 Cov.: 32 AF XY: 0.247 AC XY: 18358 AN XY: 74194

African (AFR) AF: 0.0882 AC: 3660 AN: 41506

American (AMR) AF: 0.320 AC: 4876 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2124 AN: 5148

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3427 AN: 10518

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19878 AN: 67882

Other (OTH) AF: 0.246 AC: 517 AN: 2104

Alfa AF: 0.263 Hom.: 11959

Bravo AF: 0.233

Asia WGS AF: 0.311 AC: 1078 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs12527818; hg19: chr6-93911119; COSMIC: COSV62933159;