rs7228911

Positions:

• chr18-10353782-T-C

Variant summary

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

The ENST00000582531.1(ENSG00000264876):​n.264-14834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 152,258 control chromosomes in the GnomAD database, including 256 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 0.054 (256 hom., cov: 33)
• Consequence: ENSG00000264876 ENST00000582531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

Genes affected

ENSG00000264876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371986	XR_001753347.1	n.1278-14834A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000264876	ENST00000582531.1	n.264-14834A>G		intron_variant		5
ENSG00000264876	ENST00000666410.1	n.271-14834A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8246 AN: 152140 Hom.: 256 Cov.: 33

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.00980

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0460

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

GnomAD4 genome AF: 0.0542 AC: 8248 AN: 152258 Hom.: 256 Cov.: 33 AF XY: 0.0541 AC XY: 4030 AN XY: 74454

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.00963

Gnomad4 SAS AF: 0.0352

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0465 Hom.: 248

Bravo AF: 0.0531

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.4
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7228911; hg19: chr18-10353779;