6-99224138-T-C

Position:

• chr6-99224138-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.99224138T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.350

Alfa AF: 0.336 Hom.: 20465

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

Splicing

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

Publications

LitVar

Other links and lift over

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