19-31692447-G-C

Variant names:

• chr19-31692447-G-C
• rs10500254
• ENST00000770546.1:n.385+35591C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000770546.1(ENSG00000300274):​n.385+35591C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00611 in 152,164 control chromosomes in the GnomAD database, including 6 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 0.0061 (6 hom., cov: 32)
• Consequence: ENSG00000300274 ENST00000770546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 0 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=-0.97).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00611 (929/152164) while in subpopulation EAS AF = 0.0472 (243/5146). AF 95% confidence interval is 0.0424. There are 6 homozygotes in GnomAd4. There are 476 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

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

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
	ENSG00000300274	ENST00000770546.1		n.385+35591C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00609 AC: 926 AN: 152046 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0123

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.00374

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00522

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.00611 AC: 929 AN: 152164 Hom.: 6 Cov.: 32 AF XY: 0.00640 AC XY: 476 AN XY: 74376

African (AFR) AF: 0.00106 AC: 44 AN: 41516

American (AMR) AF: 0.0124 AC: 189 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00115 AC: 4 AN: 3470

East Asian (EAS) AF: 0.0472 AC: 243 AN: 5146

South Asian (SAS) AF: 0.00395 AC: 19 AN: 4812

European-Finnish (FIN) AF: 0.00528 AC: 56 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00522 AC: 355 AN: 68012

Other (OTH) AF: 0.00804 AC: 17 AN: 2114

Alfa AF: 0.00219 Hom.: 0

Bravo AF: 0.00752

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0050
DANN	Benign	0.41
PhyloP100		-1.5

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: rs10500254;

hg19: chr19-32183353;