rs1819788

Variant names:

• chr6-31291360-T-C
• rs1819788
• ENST00000755297.1:n.32+20254T>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+20254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 149,168 control chromosomes in the GnomAD database, including 900 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 0.10 (900 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 7 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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
ENSG00000298396	ENST00000755297.1	n.32+20254T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15559 AN: 149052 Hom.: 901 Cov.: 31

Gnomad AFR AF: 0.0770

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0548

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.104 AC: 15556 AN: 149168 Hom.: 900 Cov.: 31 AF XY: 0.0990 AC XY: 7201 AN XY: 72768

African (AFR) AF: 0.0769 AC: 3107 AN: 40414

American (AMR) AF: 0.117 AC: 1744 AN: 14852

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3448

East Asian (EAS) AF: 0.107 AC: 527 AN: 4934

South Asian (SAS) AF: 0.0729 AC: 336 AN: 4610

European-Finnish (FIN) AF: 0.0516 AC: 531 AN: 10298

Middle Eastern (MID) AF: 0.0483 AC: 14 AN: 290

European-Non Finnish (NFE) AF: 0.125 AC: 8425 AN: 67340

Other (OTH) AF: 0.114 AC: 236 AN: 2078

Alfa AF: 0.105 Hom.: 655

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1819788; hg19: chr6-31259137;