19-30994967-T-C

Variant names:

• chr19-30994967-T-C
• rs276776

Variant summary

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

The variant allele was found at a frequency of 0.249 in 152,080 control chromosomes in the GnomAD database, including 4,915 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 0.25 (4915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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: 0.249 AC: 37802 AN: 151962 Hom.: 4908 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.249 AC: 37842 AN: 152080 Hom.: 4915 Cov.: 33 AF XY: 0.253 AC XY: 18828 AN XY: 74370

African (AFR) AF: 0.289 AC: 11985 AN: 41466

American (AMR) AF: 0.232 AC: 3548 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 827 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1731 AN: 5182

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2839 AN: 10558

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14435 AN: 67992

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.226 Hom.: 508

Bravo AF: 0.248

Asia WGS AF: 0.312 AC: 1085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	6.4
DANN	Benign	0.81
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs276776; hg19: chr19-31485873;