chr19-31713405-A-G

Variant names:

• chr19-31713405-A-G
• rs10417470
• ENST00000770546.1:n.385+14633T>C

Variant summary

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

The ENST00000770546.1(ENSG00000300274):​n.385+14633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,966 control chromosomes in the GnomAD database, including 15,017 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 (15017 hom., cov: 32)
• Consequence: ENSG00000300274 ENST00000770546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 3 publications found

Genes affected

ENSG00000300274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770546.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300274	ENST00000770546.1		n.385+14633T>C		intron	N/A
	ENSG00000300290	ENST00000770631.1		n.318-171A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63283 AN: 151848 Hom.: 14977 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.417 AC: 63381 AN: 151966 Hom.: 15017 Cov.: 32 AF XY: 0.413 AC XY: 30641 AN XY: 74268

African (AFR) AF: 0.650 AC: 26919 AN: 41444

American (AMR) AF: 0.373 AC: 5695 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1812 AN: 5138

South Asian (SAS) AF: 0.419 AC: 2014 AN: 4802

European-Finnish (FIN) AF: 0.217 AC: 2299 AN: 10576

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22366 AN: 67946

Other (OTH) AF: 0.384 AC: 812 AN: 2114

Alfa AF: 0.359 Hom.: 19707

Bravo AF: 0.433

Asia WGS AF: 0.434 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.44
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10417470; hg19: chr19-32204311;