rs7248321

Variant names:

• chr19-50915249-T-C
• rs7248321

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 0.0747 in 152,220 control chromosomes in the GnomAD database, including 649 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 0.075 (649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11351 AN: 152102 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0747 AC: 11374 AN: 152220 Hom.: 649 Cov.: 32 AF XY: 0.0727 AC XY: 5411 AN XY: 74436

African (AFR) AF: 0.166 AC: 6895 AN: 41500

American (AMR) AF: 0.0417 AC: 637 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4822

European-Finnish (FIN) AF: 0.0300 AC: 319 AN: 10620

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3130 AN: 68016

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0532 Hom.: 535

Bravo AF: 0.0794

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.8
DANN	Benign	0.38
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7248321; hg19: chr19-51418505;