11-33398618-C-T

Position:

• chr11-33398618-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012194.3(KIAA1549L):​c.238+21729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,116 control chromosomes in the GnomAD database, including 19,122 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 (19122 hom., cov: 32)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

KIAA1549L (HGNC:24836): (KIAA1549 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1549L	NM_012194.3	c.238+21729C>T		intron_variant		ENST00000658780.2	NP_036326.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1549L	ENST00000658780.2	c.238+21729C>T		intron_variant			NM_012194.3	ENSP00000499430.1
KIAA1549L	ENST00000526400.7	c.238+21729C>T		intron_variant		5		ENSP00000433481.3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71002 AN: 151998 Hom.: 19127 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.467 AC: 70997 AN: 152116 Hom.: 19122 Cov.: 32 AF XY: 0.471 AC XY: 35021 AN XY: 74356

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.491

Alfa AF: 0.549 Hom.: 5994

Bravo AF: 0.448

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10501129; hg19: chr11-33420164;