7-49233248-C-T

Variant names:

• chr7-49233248-C-T
• rs4529412
• ENST00000440455.1:n.198+2914C>T

Variant summary

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

The ENST00000440455.1(ENSG00000234686):​n.198+2914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,180 control chromosomes in the GnomAD database, including 2,529 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 0.18 (2529 hom., cov: 32)
• Consequence: ENSG00000234686 ENST00000440455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 1 publications found

Genes affected

ENSG00000234686 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.221 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
ENSG00000234686	ENST00000440455.1	n.198+2914C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27108 AN: 152062 Hom.: 2527 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.178 AC: 27136 AN: 152180 Hom.: 2529 Cov.: 32 AF XY: 0.180 AC XY: 13384 AN XY: 74394

African (AFR) AF: 0.172 AC: 7157 AN: 41520

American (AMR) AF: 0.228 AC: 3482 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 578 AN: 3472

East Asian (EAS) AF: 0.0171 AC: 89 AN: 5192

South Asian (SAS) AF: 0.163 AC: 786 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2487 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11941 AN: 67986

Other (OTH) AF: 0.173 AC: 366 AN: 2116

Alfa AF: 0.177 Hom.: 1854

Bravo AF: 0.176

Asia WGS AF: 0.118 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.51
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs4529412; hg19: chr7-49272844;