ENST00000419813.2:n.2769A>G

Variant names:

• chr7-23101028-T-C
• rs1468592
• ENST00000419813.2:n.2769A>G

Variant summary

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

The ENST00000419813.2(KLHL7-DT):​n.2769A>G 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 0.444 in 151,012 control chromosomes in the GnomAD database, including 17,087 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 0.44 (17087 hom., cov: 32)
• Consequence: KLHL7-DT ENST00000419813.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

KLHL7-DT (HGNC:43431): (KLHL7 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -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 = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHL7-DT	NR_046220.1	n.*200A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHL7-DT	ENST00000419813.2	n.2769A>G		non_coding_transcript_exon_variant	Exon 3 of 3	2
KLHL7-DT	ENST00000662806.1	n.2764A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 66930 AN: 150894 Hom.: 17049 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.444 AC: 67012 AN: 151012 Hom.: 17087 Cov.: 32 AF XY: 0.435 AC XY: 32126 AN XY: 73818

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.453

Alfa AF: 0.379 Hom.: 5872

Bravo AF: 0.457

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468592; hg19: chr7-23140647;