chr3-55170106-A-G

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906243	XR_007095917.1	n.159-26184T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239991	ENST00000485347.1	n.221+1097T>C		intron_variant	Intron 2 of 2	3
ENSG00000239991	ENST00000810770.1	n.450+1097T>C		intron_variant	Intron 3 of 3
ENSG00000239991	ENST00000810771.1	n.123+1097T>C		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs716540; hg19: chr3-55204134;