rs10488077

Variant names:

• chr7-23104563-A-T
• rs10488077
• ENST00000419813.2:n.151-246T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419813.2(KLHL7-DT):​n.151-246T>A variant causes a intron 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 ENST00000419813.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419813.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLHL7-DT	NR_046220.1		n.146-246T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLHL7-DT	ENST00000419813.2	TSL:2	n.151-246T>A		intron	N/A
	KLHL7-DT	ENST00000662806.1		n.146-246T>A		intron	N/A
	KLHL7-DT	ENST00000753833.1		n.92-246T>A		intron	N/A

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

African (AFR) AF: 0.449 AC: 18127 AN: 40382

American (AMR) AF: 0.312 AC: 4753 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1343 AN: 3466

East Asian (EAS) AF: 0.169 AC: 875 AN: 5182

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4818

European-Finnish (FIN) AF: 0.299 AC: 3158 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25386 AN: 67934

Other (OTH) AF: 0.403 AC: 848 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.56
PhyloP100		-0.033

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10488077;

hg19: chr7-23144182;