rs7249968

Positions:

• chr19-30220335-T-C

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, non coding transcript 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: ENST00000588092.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000588092.1	n.296-545A>G		intron_variant, non_coding_transcript_variant		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;