ENST00000718234.1:n.319+38316T>C

Variant names:

• chr7-24281041-A-G
• rs7800861
• ENST00000718234.1:n.319+38316T>C

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+38316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,988 control chromosomes in the GnomAD database, including 7,189 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 0.30 (7189 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 3 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+38316T>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-84012T>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+38316T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000718234.1	n.319+38316T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+38316T>C		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+38316T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.329-11211T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45418 AN: 151870 Hom.: 7172 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.299 AC: 45469 AN: 151988 Hom.: 7189 Cov.: 32 AF XY: 0.297 AC XY: 22110 AN XY: 74326

African (AFR) AF: 0.407 AC: 16861 AN: 41402

American (AMR) AF: 0.227 AC: 3468 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1607 AN: 5170

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4814

European-Finnish (FIN) AF: 0.250 AC: 2648 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17462 AN: 67958

Other (OTH) AF: 0.300 AC: 634 AN: 2112

Alfa AF: 0.283 Hom.: 856

Bravo AF: 0.302

Asia WGS AF: 0.316 AC: 1096 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.88
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7800861; hg19: chr7-24320660;