rs7247551

Variant names:

• chr19-44951509-G-A
• rs7247551
• ENST00000591646.1:n.114-483C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591646.1(ENSG00000267114):​n.114-483C>T variant causes a intron 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: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 9 publications found

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267114	ENST00000591646.1	n.114-483C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.775 AC: 32020 AN: 41322

American (AMR) AF: 0.679 AC: 10334 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3464

East Asian (EAS) AF: 0.625 AC: 3203 AN: 5124

South Asian (SAS) AF: 0.635 AC: 3061 AN: 4818

European-Finnish (FIN) AF: 0.521 AC: 5468 AN: 10504

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33926 AN: 67830

Other (OTH) AF: 0.579 AC: 1220 AN: 2108

Alfa AF: 0.614 Hom.: 11808

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
PhyloP100		0.46

Splicing

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

Other links and lift over

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