rs278191

Variant names:

• chr19-30932715-C-T
• rs278191
• ENST00000827556.1:n.500+6239C>T

Variant summary

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

The ENST00000827556.1(ENSG00000267378):​n.500+6239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,102 control chromosomes in the GnomAD database, including 763 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 0.077 (763 hom., cov: 32)
• Consequence: ENSG00000267378 ENST00000827556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 0 publications found

Genes affected

ENSG00000267378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827556.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267378	ENST00000827556.1		n.500+6239C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11709 AN: 151982 Hom.: 762 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0771 AC: 11721 AN: 152102 Hom.: 763 Cov.: 32 AF XY: 0.0765 AC XY: 5684 AN XY: 74348

African (AFR) AF: 0.185 AC: 7663 AN: 41460

American (AMR) AF: 0.0454 AC: 694 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0856 AC: 297 AN: 3470

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5164

South Asian (SAS) AF: 0.0497 AC: 239 AN: 4810

European-Finnish (FIN) AF: 0.0356 AC: 377 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0296 AC: 2016 AN: 67998

Other (OTH) AF: 0.0824 AC: 174 AN: 2112

Alfa AF: 0.0403 Hom.: 368

Bravo AF: 0.0831

Asia WGS AF: 0.0500 AC: 173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.57
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs278191; hg19: chr19-31423621;