rs724841

Variant names:

• chr2-107003786-G-A
• rs724841
• ENST00000727380.1:n.*87C>T

Variant summary

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

The ENST00000727380.1(ENSG00000295016):​n.*87C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,056 control chromosomes in the GnomAD database, including 5,964 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 0.26 (5964 hom., cov: 32)
• Consequence: ENSG00000295016 ENST00000727380.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

Genes affected

ENSG00000295016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727380.1. 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
	ENSG00000295016	ENST00000727380.1		n.*87C>T		downstream_gene	N/A
	ENSG00000295016	ENST00000727381.1		n.*81C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40278 AN: 151938 Hom.: 5967 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.265 AC: 40279 AN: 152056 Hom.: 5964 Cov.: 32 AF XY: 0.264 AC XY: 19605 AN XY: 74328

African (AFR) AF: 0.141 AC: 5847 AN: 41482

American (AMR) AF: 0.257 AC: 3927 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1545 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1314 AN: 5156

South Asian (SAS) AF: 0.266 AC: 1281 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2739 AN: 10554

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22669 AN: 67976

Other (OTH) AF: 0.284 AC: 598 AN: 2108

Alfa AF: 0.312 Hom.: 4888

Bravo AF: 0.258

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs724841; hg19: chr2-107620242;