chr2-148875136-C-A

Position:

• chr2-148875136-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The XR_001739733.2(KIF5C-AS1):​n.8182G>T 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 0.0202 in 108,672 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.020 (26 hom., cov: 29)
  • Exomes 𝑓: 0.014 (0 hom.)
• Consequence: KIF5C-AS1 XR_001739733.2 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.378

Genes affected

KIF5C-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant 2-148875136-C-A is Benign according to our data. Variant chr2-148875136-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 679867.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0203 (2180/107504) while in subpopulation AMR AF= 0.0307 (247/8040). AF 95% confidence interval is 0.0276. There are 26 homozygotes in gnomad4. There are 1042 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF5C-AS1	XR_001739733.2	n.8182G>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5C-AS1	ENST00000601658.5	n.676+2090G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0203 AC: 2180 AN: 107476 Hom.: 26 Cov.: 29

Gnomad AFR AF: 0.00596

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00808

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.0704

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0319

GnomAD4 exome AF: 0.0137 AC: 16 AN: 1168 Hom.: 0 AF XY: 0.0149 AC XY: 10 AN XY: 672

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0148

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0203 AC: 2180 AN: 107504 Hom.: 26 Cov.: 29 AF XY: 0.0209 AC XY: 1042 AN XY: 49960

Gnomad4 AFR AF: 0.00599

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0563

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00809

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0245

Gnomad4 OTH AF: 0.0316

Alfa AF: 0.0169 Hom.: 2

Bravo AF: 0.0149

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149307156; hg19: chr2-149632705;