rs7248668

Positions:

• chr19-39253181-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.156 in 152,120 control chromosomes in the GnomAD database, including 2,237 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 0.16 (2237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23786 AN: 152004 Hom.: 2238 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.156 AC: 23796 AN: 152120 Hom.: 2237 Cov.: 32 AF XY: 0.153 AC XY: 11375 AN XY: 74382

Gnomad4 AFR AF: 0.0685

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0658

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.175

Alfa AF: 0.162 Hom.: 328

Bravo AF: 0.165

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7248668; hg19: chr19-39743821;