6-99224138-T-C

Variant names:

• chr6-99224138-T-C
• rs2132683

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 0.379 in 152,012 control chromosomes in the GnomAD database, including 11,212 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 0.38 (11212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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: 0.379 AC: 57576 AN: 151894 Hom.: 11194 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.379 AC: 57644 AN: 152012 Hom.: 11212 Cov.: 32 AF XY: 0.382 AC XY: 28403 AN XY: 74276

African (AFR) AF: 0.447 AC: 18537 AN: 41452

American (AMR) AF: 0.418 AC: 6381 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3464

East Asian (EAS) AF: 0.501 AC: 2591 AN: 5172

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4824

European-Finnish (FIN) AF: 0.408 AC: 4306 AN: 10546

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22305 AN: 67960

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.345 Hom.: 43422

Bravo AF: 0.389

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2132683; hg19: chr6-99672014; COSMIC: COSV60254172;