19-49727070-C-G

Variant names:

• chr19-49727070-C-G
• rs8102150
• ENST00000730480.1:n.696-235C>G

Variant summary

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

The ENST00000730480.1(ENSG00000295494):​n.696-235C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 151,952 control chromosomes in the GnomAD database, including 1,230 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 0.092 (1230 hom., cov: 31)
• Consequence: ENSG00000295494 ENST00000730480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 3 publications found

Genes affected

ENSG00000295494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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
ENSG00000295494	ENST00000730480.1	n.696-235C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13882 AN: 151834 Hom.: 1224 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0916 AC: 13915 AN: 151952 Hom.: 1230 Cov.: 31 AF XY: 0.0916 AC XY: 6800 AN XY: 74258

African (AFR) AF: 0.216 AC: 8928 AN: 41426

American (AMR) AF: 0.124 AC: 1892 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.154 AC: 796 AN: 5172

South Asian (SAS) AF: 0.0652 AC: 314 AN: 4818

European-Finnish (FIN) AF: 0.0110 AC: 116 AN: 10570

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

European-Non Finnish (NFE) AF: 0.0196 AC: 1330 AN: 67964

Other (OTH) AF: 0.0831 AC: 175 AN: 2106

Alfa AF: 0.0175 Hom.: 11

Bravo AF: 0.108

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs8102150; hg19: chr19-50230327;