chr19-31667558-A-G

Variant names:

• chr19-31667558-A-G
• rs16966122
• ENST00000770546.1:n.386-24898T>C

Variant summary

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

The ENST00000770546.1(ENSG00000300274):​n.386-24898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,214 control chromosomes in the GnomAD database, including 1,747 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 0.15 (1747 hom., cov: 32)
• Consequence: ENSG00000300274 ENST00000770546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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
ENSG00000300274	ENST00000770546.1	n.386-24898T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22398 AN: 152096 Hom.: 1737 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.147 AC: 22435 AN: 152214 Hom.: 1747 Cov.: 32 AF XY: 0.146 AC XY: 10838 AN XY: 74418

African (AFR) AF: 0.169 AC: 7032 AN: 41516

American (AMR) AF: 0.0988 AC: 1510 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3470

East Asian (EAS) AF: 0.0933 AC: 484 AN: 5186

South Asian (SAS) AF: 0.112 AC: 542 AN: 4824

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10532 AN: 68010

Other (OTH) AF: 0.119 AC: 251 AN: 2112

Alfa AF: 0.147 Hom.: 5169

Bravo AF: 0.147

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs16966122; hg19: chr19-32158464;