rs7246045

Variant names:

• chr19-49042825-T-G
• rs7246045

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 0.00887 in 629,238 control chromosomes in the GnomAD database, including 244 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 0.027 (184 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (60 hom.)
• Consequence: LOC100287453 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 2 publications found

Genes affected

LOC100287453 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287453		n.49042825T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268669	ENST00000593746.1	n.*94T>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4135 AN: 152010 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0211

GnomAD4 exome AF: 0.00300 AC: 1429 AN: 477110 Hom.: 60 AF XY: 0.00259 AC XY: 642 AN XY: 247920

African (AFR) AF: 0.0855 AC: 1059 AN: 12386

American (AMR) AF: 0.00519 AC: 101 AN: 19456

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12866

East Asian (EAS) AF: 0.000586 AC: 16 AN: 27284

South Asian (SAS) AF: 0.00107 AC: 45 AN: 41998

European-Finnish (FIN) AF: 0.0000767 AC: 2 AN: 26074

Middle Eastern (MID) AF: 0.00372 AC: 7 AN: 1882

European-Non Finnish (NFE) AF: 0.000152 AC: 47 AN: 310158

Other (OTH) AF: 0.00608 AC: 152 AN: 25006

GnomAD4 genome AF: 0.0273 AC: 4155 AN: 152128 Hom.: 184 Cov.: 32 AF XY: 0.0267 AC XY: 1989 AN XY: 74392

African (AFR) AF: 0.0940 AC: 3898 AN: 41464

American (AMR) AF: 0.0112 AC: 171 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5164

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 67994

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0240 Hom.: 17

Bravo AF: 0.0313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7246045; hg19: chr19-49546082;