NM_012194.3:c.4079-1412A>G

Variant names:

• chr11-33566664-A-G
• rs10437629
• NM_012194.3:c.4079-1412A>G

Variant summary

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

The NM_012194.3(KIAA1549L):​c.4079-1412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,154 control chromosomes in the GnomAD database, including 6,950 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 0.22 (6950 hom., cov: 32)
• Consequence: KIAA1549L NM_012194.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1549L	NM_012194.3	c.4079-1412A>G		intron_variant	Intron 8 of 20	ENST00000658780.2	NP_036326.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1549L	ENST00000658780.2	c.4079-1412A>G		intron_variant	Intron 8 of 20		NM_012194.3	ENSP00000499430.1
KIAA1549L	ENST00000321505.9	c.3188-1412A>G		intron_variant	Intron 7 of 19	1		ENSP00000315295.4
KIAA1549L	ENST00000526400.7	c.1889-1412A>G		intron_variant	Intron 8 of 20	5		ENSP00000433481.3
KIAA1549L	ENST00000265654.6	c.3329-1412A>G		intron_variant	Intron 7 of 10	2		ENSP00000265654.6

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33516 AN: 152036 Hom.: 6923 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.221 AC: 33594 AN: 152154 Hom.: 6950 Cov.: 32 AF XY: 0.220 AC XY: 16374 AN XY: 74388

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0995

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.196

Alfa AF: 0.101 Hom.: 2102

Bravo AF: 0.234

Asia WGS AF: 0.278 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.0
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs10437629; hg19: chr11-33588210;