chr19-2484808-T-C

Variant names:

• chr19-2484808-T-C
• rs929461
• ENST00000776227.1:n.262-6322A>G

Variant summary

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

The ENST00000776227.1(ENSG00000301105):​n.262-6322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,166 control chromosomes in the GnomAD database, including 1,182 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 0.12 (1182 hom., cov: 32)
• Consequence: ENSG00000301105 ENST00000776227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 2 publications found

Genes affected

ENSG00000301105 (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 = 0.157 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
ENSG00000301105	ENST00000776227.1	n.262-6322A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18287 AN: 152048 Hom.: 1181 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.120 AC: 18309 AN: 152166 Hom.: 1182 Cov.: 32 AF XY: 0.119 AC XY: 8861 AN XY: 74406

African (AFR) AF: 0.161 AC: 6666 AN: 41498

American (AMR) AF: 0.0715 AC: 1093 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3466

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4818

European-Finnish (FIN) AF: 0.120 AC: 1269 AN: 10602

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8251 AN: 67986

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.116 Hom.: 1996

Bravo AF: 0.120

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.67
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs929461; hg19: chr19-2484806;