rs7247551

Positions:

• chr19-44951509-G-A
• chr19-44951509-G-C

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-483C>T 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 0.603 in 151,584 control chromosomes in the GnomAD database, including 28,888 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 0.60 (28888 hom., cov: 30)
• Consequence: ENST00000591646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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.114-483C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91374 AN: 151464 Hom.: 28836 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.603 AC: 91480 AN: 151584 Hom.: 28888 Cov.: 30 AF XY: 0.605 AC XY: 44787 AN XY: 74058

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.579

Alfa AF: 0.574 Hom.: 3373

Bravo AF: 0.624

Asia WGS AF: 0.657 AC: 2286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7247551; hg19: chr19-45454766; COSMIC: COSV52991020;