rs7249968

Variant names:

• chr19-30220335-T-C
• rs7249968
• ENST00000588092.1:n.296-545A>G

Variant summary

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

The ENST00000588092.1(ENSG00000267223):​n.296-545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,700 control chromosomes in the GnomAD database, including 5,124 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 0.25 (5124 hom., cov: 31)
• Consequence: ENSG00000267223 ENST00000588092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

ENSG00000267223 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000267223	ENST00000588092.1	n.296-545A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38392 AN: 151582 Hom.: 5114 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.253 AC: 38437 AN: 151700 Hom.: 5124 Cov.: 31 AF XY: 0.255 AC XY: 18875 AN XY: 74136

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.274

Alfa AF: 0.237 Hom.: 5500

Bravo AF: 0.261

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7249968; hg19: chr19-30711242;