rs2685056

Variant names:

• chr3-104699729-G-A
• rs2685056
• ENST00000721885.1:n.502-69150C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-104699729-G-A
• chr3-104699729-G-C
• chr3-104699729-G-T

Variant summary

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

The ENST00000721885.1(ENSG00000294208):​n.502-69150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,610 control chromosomes in the GnomAD database, including 20,799 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 0.50 (20799 hom., cov: 32)
• Consequence: ENSG00000294208 ENST00000721885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744
• Publications: 4 publications found

Genes affected

ENSG00000294208 (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 (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721885.1. 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
	ENSG00000294208	ENST00000721885.1		n.502-69150C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75707 AN: 151492 Hom.: 20762 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.500 AC: 75798 AN: 151610 Hom.: 20799 Cov.: 32 AF XY: 0.502 AC XY: 37189 AN XY: 74088

African (AFR) AF: 0.711 AC: 29418 AN: 41374

American (AMR) AF: 0.445 AC: 6777 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4183 AN: 5156

South Asian (SAS) AF: 0.579 AC: 2785 AN: 4814

European-Finnish (FIN) AF: 0.378 AC: 3962 AN: 10478

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25662 AN: 67806

Other (OTH) AF: 0.478 AC: 1005 AN: 2102

Alfa AF: 0.415 Hom.: 45142

Bravo AF: 0.515

Asia WGS AF: 0.687 AC: 2384 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.18
PhyloP100		0.74

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: rs2685056;

hg19: chr3-104418573;