rs3794668

Variant names:

• chr16-87710885-T-A
• rs3794668
• NM_017566.4:c.1044+350A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-87710885-T-A
• chr16-87710885-T-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_017566.4(KLHDC4):​c.1044+350A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KLHDC4 NM_017566.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

Genes affected

KLHDC4 (HGNC:25272): (kelch domain containing 4)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLHDC4	NM_017566.4	c.1044+350A>T		intron_variant	Intron 9 of 11	ENST00000270583.10	NP_060036.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLHDC4	ENST00000270583.10	c.1044+350A>T		intron_variant	Intron 9 of 11	1	NM_017566.4	ENSP00000270583.4
KLHDC4	ENST00000567298.5	n.1044+350A>T		intron_variant	Intron 9 of 16	5		ENSP00000457570.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 152002 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 74776 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 38624

African (AFR) AF: 0.00 AC: 0 AN: 3392

American (AMR) AF: 0.00 AC: 0 AN: 5088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2076

East Asian (EAS) AF: 0.00 AC: 0 AN: 5376

South Asian (SAS) AF: 0.00 AC: 0 AN: 7026

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2592

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 324

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 44764

Other (OTH) AF: 0.00 AC: 0 AN: 4138

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 152002 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74210

African (AFR) AF: 0.00 AC: 0 AN: 41400

American (AMR) AF: 0.00 AC: 0 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67982

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.00 Hom.: 13303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3794668; hg19: chr16-87744491;