chr19-31675940-T-G

Variant names:

• chr19-31675940-T-G
• rs8104309
• ENST00000770546.1:n.386-33280A>C

Variant summary

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

The ENST00000770546.1(ENSG00000300274):​n.386-33280A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,092 control chromosomes in the GnomAD database, including 2,637 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 0.18 (2637 hom., cov: 30)
• Consequence: ENSG00000300274 ENST00000770546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 1 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).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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.386-33280A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26576 AN: 151974 Hom.: 2614 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.175 AC: 26640 AN: 152092 Hom.: 2637 Cov.: 30 AF XY: 0.172 AC XY: 12805 AN XY: 74348

African (AFR) AF: 0.258 AC: 10700 AN: 41470

American (AMR) AF: 0.110 AC: 1682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3468

East Asian (EAS) AF: 0.0983 AC: 508 AN: 5166

South Asian (SAS) AF: 0.115 AC: 554 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10737 AN: 67992

Other (OTH) AF: 0.138 AC: 291 AN: 2102

Alfa AF: 0.157 Hom.: 1004

Bravo AF: 0.178

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs8104309; hg19: chr19-32166846;