rs716540

Variant names:

• chr3-55170106-A-G
• rs716540
• ENST00000485347.1:n.221+1097T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-55170106-A-G
• chr3-55170106-A-T

Variant summary

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

The ENST00000485347.1(ENSG00000239991):​n.221+1097T>C variant causes a intron change. The variant allele was found at a frequency of 0.498 in 152,076 control chromosomes in the GnomAD database, including 19,099 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 (19099 hom., cov: 33)
• Consequence: ENSG00000239991 ENST00000485347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.52
• Publications: 6 publications found

Genes affected

ENSG00000239991 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485347.1. 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
	ENSG00000239991	ENST00000485347.1	TSL:3	n.221+1097T>C		intron	N/A
	ENSG00000239991	ENST00000810770.1		n.450+1097T>C		intron	N/A
	ENSG00000239991	ENST00000810771.1		n.123+1097T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75727 AN: 151958 Hom.: 19070 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.498 AC: 75808 AN: 152076 Hom.: 19099 Cov.: 33 AF XY: 0.503 AC XY: 37390 AN XY: 74326

African (AFR) AF: 0.520 AC: 21555 AN: 41486

American (AMR) AF: 0.516 AC: 7875 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1358 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3403 AN: 5174

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4820

European-Finnish (FIN) AF: 0.545 AC: 5752 AN: 10560

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32174 AN: 67978

Other (OTH) AF: 0.504 AC: 1067 AN: 2116

Alfa AF: 0.472 Hom.: 10938

Bravo AF: 0.498

Asia WGS AF: 0.550 AC: 1911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.76
PhyloP100		5.5

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: rs716540;

hg19: chr3-55204134;