rs2761210

Positions:

• chr11-33385425-C-A

Variant summary

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

The NM_012194.3(KIAA1549L):​c.238+8536C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,024 control chromosomes in the GnomAD database, including 30,253 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 0.63 (30253 hom., cov: 31)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1549L	NM_012194.3	c.238+8536C>A		intron_variant		ENST00000658780.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1549L	ENST00000658780.2	c.238+8536C>A		intron_variant			NM_012194.3	P2
KIAA1549L	ENST00000526400.7	c.238+8536C>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95472 AN: 151906 Hom.: 30238 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.628 AC: 95516 AN: 152024 Hom.: 30253 Cov.: 31 AF XY: 0.627 AC XY: 46599 AN XY: 74320

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.630

Alfa AF: 0.646 Hom.: 9490

Bravo AF: 0.623

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2761210; hg19: chr11-33406971;