2-210144383-T-C

Variant names:

• chr2-210144383-T-C
• rs10932320
• NM_152519.4:c.1088+9112A>G

Variant summary

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

The NM_152519.4(KANSL1L):​c.1088+9112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,074 control chromosomes in the GnomAD database, including 19,629 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 0.47 (19629 hom., cov: 32)
• Consequence: KANSL1L NM_152519.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 2 publications found

Genes affected

KANSL1L (HGNC:26310): (KAT8 regulatory NSL complex subunit 1 like) Predicted to enable histone acetyltransferase binding activity. Predicted to be part of NSL complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KANSL1L	NM_152519.4	c.1088+9112A>G		intron_variant	Intron 2 of 14	ENST00000281772.14	NP_689732.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KANSL1L	ENST00000281772.14	c.1088+9112A>G		intron_variant	Intron 2 of 14	5	NM_152519.4	ENSP00000281772.8

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72129 AN: 151956 Hom.: 19616 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.474 AC: 72159 AN: 152074 Hom.: 19629 Cov.: 32 AF XY: 0.479 AC XY: 35585 AN XY: 74322

African (AFR) AF: 0.181 AC: 7513 AN: 41502

American (AMR) AF: 0.599 AC: 9136 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2489 AN: 5172

South Asian (SAS) AF: 0.561 AC: 2702 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6143 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40497 AN: 67970

Other (OTH) AF: 0.500 AC: 1057 AN: 2112

Alfa AF: 0.516 Hom.: 3195

Bravo AF: 0.460

Asia WGS AF: 0.520 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.11
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: rs10932320; hg19: chr2-211009107;