6-24358255-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000274766.2(KAAG1):n.1353G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 224,744 control chromosomes in the GnomAD database, including 105,029 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.96 (69875 hom., cov: 31)
  • Exomes 𝑓: 0.98 (35154 hom.)
• Consequence: KAAG1 ENST00000274766.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.177

Genes affected

KAAG1 (HGNC:21031): (kidney associated DCDC2 antisense RNA 1)

DCDC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-24358255-G-C is Benign according to our data. Variant chr6-24358255-G-C is described in ClinVar as [Benign]. Clinvar id is 1255344.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KAAG1	NR_174942.1	n.1353G>C		non_coding_transcript_exon_variant	1/1
DCDC2	NM_001195610.2	c.-97-408C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KAAG1	ENST00000274766.2	n.1353G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145576 AN: 152066 Hom.: 69841 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.962

GnomAD4 exome AF: 0.984 AC: 71411 AN: 72560 Hom.: 35154 Cov.: 1 AF XY: 0.985 AC XY: 35498 AN XY: 36046

Gnomad4 AFR exome AF: 0.886

Gnomad4 AMR exome AF: 0.971

Gnomad4 ASJ exome AF: 0.993

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.998

Gnomad4 FIN exome AF: 0.997

Gnomad4 NFE exome AF: 0.983

Gnomad4 OTH exome AF: 0.976

GnomAD4 genome AF: 0.957 AC: 145664 AN: 152184 Hom.: 69875 Cov.: 31 AF XY: 0.960 AC XY: 71408 AN XY: 74416

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.962

Alfa AF: 0.974 Hom.: 3927

Bravo AF: 0.951

Asia WGS AF: 0.993 AC: 3453 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
Dann	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1277349; hg19: chr6-24358483;