18-41607206-T-G

Variant names:

• chr18-41607206-T-G
• rs16975050
• ENST00000593577.3:n.130-12738A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000595135.5(KC6):​n.187-12738A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: KC6 ENST00000595135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.819
• Publications: 0 publications found

Genes affected

KC6 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595135.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KC6	ENST00000593577.3	TSL:4	n.130-12738A>C		intron	N/A
	KC6	ENST00000595135.5	TSL:3	n.187-12738A>C		intron	N/A
	KC6	ENST00000599934.1	TSL:4	n.125+24794A>C		intron	N/A

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

African (AFR) AF: 0.202 AC: 8368 AN: 41506

American (AMR) AF: 0.0305 AC: 466 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3468

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5180

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4820

European-Finnish (FIN) AF: 0.00367 AC: 39 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 950 AN: 68026

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0320 Hom.: 901

Bravo AF: 0.0754

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.64
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs16975050; hg19: chr18-39187170;