rs7248162

Positions:

• chr19-44951429-T-C
• chr19-44951429-T-G

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-403A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,826 control chromosomes in the GnomAD database, including 21,340 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 0.52 (21340 hom., cov: 31)
• Consequence: ENST00000591646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000591646.1	n.114-403A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79241 AN: 151706 Hom.: 21305 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.522 AC: 79324 AN: 151826 Hom.: 21340 Cov.: 31 AF XY: 0.525 AC XY: 38935 AN XY: 74206

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.502

Alfa AF: 0.508 Hom.: 2611

Bravo AF: 0.534

Asia WGS AF: 0.580 AC: 2016 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	9.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7248162; hg19: chr19-45454686;