22-25197691-A-T

Variant names:

• chr22-25197691-A-T
• rs763281
• NM_001145206.2:c.*5290A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001145206.2(KIAA1671):​c.*5290A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: KIAA1671 NM_001145206.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

Genes affected

KIAA1671 (HGNC:29345): (KIAA1671)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145206.2. 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
	KIAA1671	NM_001145206.2	MANE Select	c.*5290A>T		downstream_gene	N/A	NP_001138678.1	Q9BY89-1
	KIAA1671	NM_001386932.1		c.*5290A>T		downstream_gene	N/A	NP_001373861.1	Q9BY89-1
	KIAA1671	NM_001386933.1		c.*5290A>T		downstream_gene	N/A	NP_001373862.1	Q9BY89-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1671	ENST00000358431.8	TSL:1 MANE Select	c.*5290A>T		downstream_gene	N/A	ENSP00000351207.3	Q9BY89-1
	KIAA1671	ENST00000401395.1	TSL:1	c.*5290A>T		downstream_gene	N/A	ENSP00000385377.1	Q9BY89-2
	KIAA1671	ENST00000910712.1		c.*5290A>T		downstream_gene	N/A	ENSP00000580771.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		-0.090

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: rs763281;

hg19: chr22-25593658;