rs2615913

Variant names:

• chr11-33460412-T-A
• rs2615913
• NM_012194.3:c.239-81390T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-33460412-T-A
• chr11-33460412-T-C
• chr11-33460412-T-G

Variant summary

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

The NM_012194.3(KIAA1549L):​c.239-81390T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,932 control chromosomes in the GnomAD database, including 32,386 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 0.64 (32386 hom., cov: 31)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 2 publications found

Genes affected

KIAA1549L (HGNC:24836): (KIAA1549 like) Predicted to be integral component of membrane. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012194.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1549L	NM_012194.3	MANE Select	c.239-81390T>A		intron	N/A	NP_036326.3
	KIAA1549L	NM_001410965.1		c.239-81390T>A		intron	N/A	NP_001397894.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1549L	ENST00000658780.2	MANE Select	c.239-81390T>A		intron	N/A	ENSP00000499430.1
	KIAA1549L	ENST00000526400.7	TSL:5	c.239-81390T>A		intron	N/A	ENSP00000433481.3

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97644 AN: 151814 Hom.: 32351 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.643 AC: 97731 AN: 151932 Hom.: 32386 Cov.: 31 AF XY: 0.641 AC XY: 47614 AN XY: 74276

African (AFR) AF: 0.798 AC: 33096 AN: 41452

American (AMR) AF: 0.600 AC: 9167 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2800 AN: 5156

South Asian (SAS) AF: 0.668 AC: 3218 AN: 4814

European-Finnish (FIN) AF: 0.529 AC: 5576 AN: 10548

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39790 AN: 67918

Other (OTH) AF: 0.613 AC: 1289 AN: 2104

Alfa AF: 0.604 Hom.: 3366

Bravo AF: 0.650

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.41
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2615913; hg19: chr11-33481958;