rs10488077

chr7-23104563-A-T

Variant summary

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

The NR_046220.1(KLHL7-DT):n.146-246T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 150,870 control chromosomes in the GnomAD database, including 11,262 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 0.37 (11262 hom., cov: 31)
• Consequence: KLHL7-DT NR_046220.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLHL7-DT	NR_046220.1	n.146-246T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLHL7-DT	ENST00000662806.1	n.146-246T>A		intron_variant, non_coding_transcript_variant
KLHL7-DT	ENST00000419813.2	n.151-246T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56024 AN: 150752 Hom.: 11249 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.372 AC: 56054 AN: 150870 Hom.: 11262 Cov.: 31 AF XY: 0.364 AC XY: 26809 AN XY: 73678

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.403

Alfa AF: 0.378 Hom.: 1407

Bravo AF: 0.374

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
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: rs10488077; hg19: chr7-23144182;