rs7228911

Variant names:

• chr18-10353782-T-C
• rs7228911
• ENST00000582531.1:n.264-14834A>G

Variant summary

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

The ENST00000666410.1(ENSG00000264876):​n.271-14834A>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 ENST00000666410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 0 publications found

Genes affected

ENSG00000264876 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666410.1. 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
	ENSG00000264876	ENST00000582531.1	TSL:5	n.264-14834A>G		intron	N/A
	ENSG00000264876	ENST00000666410.1		n.271-14834A>G		intron	N/A

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

African (AFR) AF: 0.0791 AC: 3286 AN: 41546

American (AMR) AF: 0.0264 AC: 404 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.00963 AC: 50 AN: 5192

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4828

European-Finnish (FIN) AF: 0.0695 AC: 737 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3299 AN: 68010

Other (OTH) AF: 0.0455 AC: 96 AN: 2110

Alfa AF: 0.0474 Hom.: 351

Bravo AF: 0.0531

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.4
DANN	Benign	0.87
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7228911;

hg19: chr18-10353779;