chr19-40864433-C-G

Variant names:

• chr19-40864433-C-G
• rs12461383
• ENST00000601627.1:n.118-27558C>G

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.118-27558C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 149,094 control chromosomes in the GnomAD database, including 15,994 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 0.42 (15994 hom., cov: 28)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 10 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.118-27558C>G		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 63182 AN: 148986 Hom.: 15988 Cov.: 28

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.424 AC: 63193 AN: 149094 Hom.: 15994 Cov.: 28 AF XY: 0.426 AC XY: 30935 AN XY: 72642

African (AFR) AF: 0.194 AC: 7873 AN: 40610

American (AMR) AF: 0.512 AC: 7678 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1712 AN: 3432

East Asian (EAS) AF: 0.320 AC: 1526 AN: 4764

South Asian (SAS) AF: 0.399 AC: 1853 AN: 4646

European-Finnish (FIN) AF: 0.559 AC: 5671 AN: 10144

Middle Eastern (MID) AF: 0.424 AC: 123 AN: 290

European-Non Finnish (NFE) AF: 0.525 AC: 35335 AN: 67244

Other (OTH) AF: 0.422 AC: 870 AN: 2060

Alfa AF: 0.458 Hom.: 2213

Bravo AF: 0.411

Asia WGS AF: 0.401 AC: 1372 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.50
PhyloP100		0.10

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

Other links and lift over

dbSNP: rs12461383; hg19: chr19-41370338;