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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593746.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268669	ENST00000593746.1	TSL:6	n.*94T>G		downstream_gene	N/A

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 v4.9

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;