XR_001745121.2:n.209+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 XR_001745121.2(LOC107986777):​n.209+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: LOC107986777 XR_001745121.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. 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
	ENSG00000228944	ENST00000718234.1		n.319+38316T>C		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+38316T>C		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+38316T>C		intron	N/A

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 v4.9

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;