19-44018761-C-T

Variant names:

• chr19-44018761-C-T
• rs6509133
• ENST00000718359.1:n.248+6169G>A

Variant summary

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

The ENST00000718359.1(ENSG00000293690):​n.248+6169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,000 control chromosomes in the GnomAD database, including 24,759 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 0.53 (24759 hom., cov: 31)
• Consequence: ENSG00000293690 ENST00000718359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 9 publications found

Genes affected

ENSG00000293690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718359.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293690	ENST00000718359.1		n.248+6169G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80522 AN: 151882 Hom.: 24762 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.530 AC: 80515 AN: 152000 Hom.: 24759 Cov.: 31 AF XY: 0.527 AC XY: 39180 AN XY: 74290

African (AFR) AF: 0.237 AC: 9813 AN: 41442

American (AMR) AF: 0.427 AC: 6523 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5168

South Asian (SAS) AF: 0.635 AC: 3060 AN: 4818

European-Finnish (FIN) AF: 0.714 AC: 7544 AN: 10564

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.706 AC: 47966 AN: 67964

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.641 Hom.: 50787

Bravo AF: 0.487

Asia WGS AF: 0.441 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.30
PhyloP100		0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6509133;

hg19: chr19-44522913;