NM_001029864.2:c.2901+1617G>T

Variant names:

• chr20-38215636-C-A
• rs6127471
• NM_001029864.2:c.2901+1617G>T

Variant summary

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

The NM_001029864.2(KIAA1755):​c.2901+1617G>T variant causes a intron 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: 31)
• Consequence: KIAA1755 NM_001029864.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 21 publications found

Genes affected

KIAA1755 (HGNC:29372): (KIAA1755)

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1755	NM_001029864.2	c.2901+1617G>T		intron_variant	Intron 13 of 13	ENST00000279024.9	NP_001025035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1755	ENST00000279024.9	c.2901+1617G>T		intron_variant	Intron 13 of 13	5	NM_001029864.2	ENSP00000279024.4
KIAA1755	ENST00000460881.5	n.1077+1224G>T		intron_variant	Intron 2 of 2	1
KIAA1755	ENST00000487506.1	n.853+1617G>T		intron_variant	Intron 1 of 1	1
KIAA1755	ENST00000484362.1	n.1180+1617G>T		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.036
DANN	Benign	0.74
PhyloP100		-1.6

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: rs6127471; hg19: chr20-36844038;