18-41607206-T-G

Position:

• chr18-41607206-T-G

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 0.0669 in 152,232 control chromosomes in the GnomAD database, including 887 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 0.067 (887 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41607206T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KC6	ENST00000593577.2	n.130-12738A>C		intron_variant		4
KC6	ENST00000595135.5	n.187-12738A>C		intron_variant		3
KC6	ENST00000599934.1	n.125+24794A>C		intron_variant		4
KC6	ENST00000600183.5	n.76+24794A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10157 AN: 152112 Hom.: 883 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00367

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0669 AC: 10178 AN: 152232 Hom.: 887 Cov.: 32 AF XY: 0.0649 AC XY: 4834 AN XY: 74436

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.0124

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.00367

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0190 Hom.: 181

Bravo AF: 0.0754

Asia WGS AF: 0.0370 AC: 129 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	2.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16975050; hg19: chr18-39187170;