22-25028863-G-C

Variant names:

• chr22-25028863-G-C
• rs534336780
• NM_001145206.2:c.864G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001145206.2(KIAA1671):​c.864G>C​(p.Thr288Thr) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. T288T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KIAA1671 NM_001145206.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36

Genes affected

KIAA1671 (HGNC:29345): (KIAA1671)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1671	NM_001145206.2	c.864G>C	p.Thr288Thr	synonymous_variant	Exon 3 of 13	ENST00000358431.8	NP_001138678.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1671	ENST00000358431.8	c.864G>C	p.Thr288Thr	synonymous_variant	Exon 3 of 13	1	NM_001145206.2	ENSP00000351207.3
KIAA1671	ENST00000406486.8	c.864G>C	p.Thr288Thr	synonymous_variant	Exon 4 of 14	5		ENSP00000385152.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 51

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.10
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs534336780; hg19: chr22-25424830;