19-3944242-G-A

Variant names:

• chr19-3944242-G-A
• rs10406174
• ENST00000691552.2:n.144+7069C>T

Variant summary

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

The ENST00000691552.2(ENSG00000289254):​n.144+7069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,846 control chromosomes in the GnomAD database, including 1,830 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 0.14 (1830 hom., cov: 30)
• Consequence: ENSG00000289254 ENST00000691552.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 10 publications found

Genes affected

ENSG00000289254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691552.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289254	ENST00000691552.2		n.144+7069C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21770 AN: 151742 Hom.: 1833 Cov.: 30

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.143 AC: 21773 AN: 151846 Hom.: 1830 Cov.: 30 AF XY: 0.144 AC XY: 10713 AN XY: 74192

African (AFR) AF: 0.233 AC: 9636 AN: 41418

American (AMR) AF: 0.0988 AC: 1504 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3464

East Asian (EAS) AF: 0.0491 AC: 253 AN: 5156

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4814

European-Finnish (FIN) AF: 0.0881 AC: 926 AN: 10516

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7358 AN: 67944

Other (OTH) AF: 0.127 AC: 267 AN: 2104

Alfa AF: 0.117 Hom.: 4055

Bravo AF: 0.142

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10406174; hg19: chr19-3944240;