rs12719740

Variant names:

• chr15-98529676-G-A
• rs12719740
• ENST00000774120.1:n.332G>A

Variant summary

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

The ENST00000774120.1(ENSG00000300802):​n.332G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,014 control chromosomes in the GnomAD database, including 3,386 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 0.21 (3386 hom., cov: 32)
• Consequence: ENSG00000300802 ENST00000774120.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 11 publications found

Genes affected

ENSG00000300802 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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
ENSG00000300802	ENST00000774120.1	n.332G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000293388	ENST00000637259.1	n.575-9287C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31580 AN: 151896 Hom.: 3383 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31597 AN: 152014 Hom.: 3386 Cov.: 32 AF XY: 0.211 AC XY: 15663 AN XY: 74298

African (AFR) AF: 0.257 AC: 10636 AN: 41430

American (AMR) AF: 0.222 AC: 3395 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3470

East Asian (EAS) AF: 0.189 AC: 980 AN: 5172

South Asian (SAS) AF: 0.196 AC: 946 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2293 AN: 10556

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12332 AN: 67988

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.187 Hom.: 12081

Bravo AF: 0.211

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12719740; hg19: chr15-99072905;