rs2615945

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012194.3(KIAA1549L):​c.238+35188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,064 control chromosomes in the GnomAD database, including 9,528 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 0.35 ( 9528 hom., cov: 32)

Consequence

KIAA1549L
NM_012194.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211
Variant links:
Genes affected
KIAA1549L (HGNC:24836): (KIAA1549 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIAA1549LNM_012194.3 linkuse as main transcriptc.238+35188G>A intron_variant ENST00000658780.2 NP_036326.3 Q6ZVL6Q12914

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIAA1549LENST00000658780.2 linkuse as main transcriptc.238+35188G>A intron_variant NM_012194.3 ENSP00000499430.1 A0A590UJI0
KIAA1549LENST00000526400.7 linkuse as main transcriptc.238+35188G>A intron_variant 5 ENSP00000433481.3 H0YDE5

Frequencies

GnomAD3 genomes
AF:
0.346
AC:
52609
AN:
151946
Hom.:
9513
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.271
Gnomad AMI
AF:
0.303
Gnomad AMR
AF:
0.348
Gnomad ASJ
AF:
0.363
Gnomad EAS
AF:
0.116
Gnomad SAS
AF:
0.303
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.397
Gnomad OTH
AF:
0.315
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.346
AC:
52646
AN:
152064
Hom.:
9528
Cov.:
32
AF XY:
0.348
AC XY:
25878
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.271
Gnomad4 AMR
AF:
0.348
Gnomad4 ASJ
AF:
0.363
Gnomad4 EAS
AF:
0.116
Gnomad4 SAS
AF:
0.304
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.397
Gnomad4 OTH
AF:
0.310
Alfa
AF:
0.380
Hom.:
23058
Bravo
AF:
0.336
Asia WGS
AF:
0.199
AC:
693
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
13
DANN
Benign
0.63

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2615945; hg19: chr11-33433623; API