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

Variant names:

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

Variant summary

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

The NM_001029864.2(KIAA1755):​c.2901+1617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,926 control chromosomes in the GnomAD database, including 13,031 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 0.40 (13031 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61236 AN: 151808 Hom.: 13033 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.403 AC: 61258 AN: 151926 Hom.: 13031 Cov.: 31 AF XY: 0.403 AC XY: 29875 AN XY: 74222

African (AFR) AF: 0.252 AC: 10447 AN: 41440

American (AMR) AF: 0.432 AC: 6601 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2699 AN: 5162

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4814

European-Finnish (FIN) AF: 0.447 AC: 4701 AN: 10524

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31900 AN: 67942

Other (OTH) AF: 0.410 AC: 863 AN: 2106

Alfa AF: 0.444 Hom.: 25450

Bravo AF: 0.399

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.076
DANN	Benign	0.76
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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;