18-41469123-A-G

Variant names:

• chr18-41469123-A-G
• rs2703175
• ENST00000593577.3:n.665+31997T>C

Variant summary

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

The ENST00000593577.3(KC6):​n.665+31997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,242 control chromosomes in the GnomAD database, including 60,083 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 0.89 (60083 hom., cov: 32)
• Consequence: KC6 ENST00000593577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593577.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KC6	ENST00000593577.3	TSL:4	n.665+31997T>C		intron	N/A
	KC6	ENST00000600644.3	TSL:3	n.935-1343T>C		intron	N/A
	ENSG00000286328	ENST00000670702.1		n.200-35011A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135040 AN: 152124 Hom.: 60036 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.888 AC: 135147 AN: 152242 Hom.: 60083 Cov.: 32 AF XY: 0.884 AC XY: 65817 AN XY: 74424

African (AFR) AF: 0.919 AC: 38183 AN: 41544

American (AMR) AF: 0.844 AC: 12908 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3044 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4270 AN: 5166

South Asian (SAS) AF: 0.801 AC: 3859 AN: 4816

European-Finnish (FIN) AF: 0.880 AC: 9343 AN: 10616

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60538 AN: 68018

Other (OTH) AF: 0.895 AC: 1888 AN: 2110

Alfa AF: 0.889 Hom.: 77803

Bravo AF: 0.886

Asia WGS AF: 0.847 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2703175; hg19: chr18-39049087;