rs2703175

Variant names:

• chr18-41469123-A-G
• rs2703175
• ENST00000600644.2:n.314-1343T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-41469123-A-G
• chr18-41469123-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000600644.2(KC6):​n.314-1343T>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 ENST00000600644.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

KC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KC6	ENST00000600644.2	n.314-1343T>C		intron_variant	Intron 1 of 1	3
ENSG00000286328	ENST00000670702.1	n.200-35011A>G		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.895

Alfa AF: 0.889 Hom.: 59606

Bravo AF: 0.886

Asia WGS AF: 0.847 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2703175; hg19: chr18-39049087;