rs1819788

Variant names:

• chr6-31291360-T-C
• rs1819788

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.114

Alfa AF: 0.116 Hom.: 316

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1819788; hg19: chr6-31259137;