rs7249968

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000267223 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588092.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267223	ENST00000588092.1	TSL:3	n.296-545A>G		intron	N/A
	ENSG00000267223	ENST00000774317.1		n.166-545A>G		intron	N/A

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

African (AFR) AF: 0.306 AC: 12639 AN: 41306

American (AMR) AF: 0.315 AC: 4803 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 792 AN: 3466

East Asian (EAS) AF: 0.160 AC: 820 AN: 5122

South Asian (SAS) AF: 0.264 AC: 1265 AN: 4800

European-Finnish (FIN) AF: 0.223 AC: 2350 AN: 10534

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14990 AN: 67918

Other (OTH) AF: 0.274 AC: 575 AN: 2096

Alfa AF: 0.235 Hom.: 14515

Bravo AF: 0.261

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.39
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7249968; hg19: chr19-30711242;