chr6-29974166-C-T

Position:

• chr6-29974166-C-T

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 0.483 in 150,646 control chromosomes in the GnomAD database, including 17,708 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 0.48 (17708 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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 (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29974166C>T		intergenic_region
MICD		n.29974166C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.482 AC: 72629 AN: 150532 Hom.: 17682 Cov.: 28

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.483 AC: 72700 AN: 150646 Hom.: 17708 Cov.: 28 AF XY: 0.480 AC XY: 35332 AN XY: 73546

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.479

Alfa AF: 0.448 Hom.: 27602

Bravo AF: 0.497

Asia WGS AF: 0.416 AC: 1445 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	0.54
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523946; hg19: chr6-29941943;