rs17041907

Variant names:

• chr3-16128121-A-C
• rs17041907
• ENST00000691919.3:n.259-9270A>C

Variant summary

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

The ENST00000691919.3(ENSG00000287042):​n.259-9270A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,086 control chromosomes in the GnomAD database, including 379 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 0.061 (379 hom., cov: 31)
• Consequence: ENSG00000287042 ENST00000691919.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 2 publications found

Genes affected

ENSG00000287042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906217	XR_007095836.1	n.86-152T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287042	ENST00000691919.3	n.259-9270A>C		intron_variant	Intron 3 of 3
ENSG00000287042	ENST00000702385.2	n.293-9270A>C		intron_variant	Intron 3 of 3
ENSG00000287042	ENST00000702609.2	n.217-9270A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9279 AN: 151968 Hom.: 378 Cov.: 31

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0610 AC: 9283 AN: 152086 Hom.: 379 Cov.: 31 AF XY: 0.0623 AC XY: 4633 AN XY: 74328

African (AFR) AF: 0.0783 AC: 3250 AN: 41484

American (AMR) AF: 0.0400 AC: 612 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5152

South Asian (SAS) AF: 0.0771 AC: 370 AN: 4796

European-Finnish (FIN) AF: 0.0627 AC: 664 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0453 AC: 3081 AN: 67994

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0488 Hom.: 325

Bravo AF: 0.0608

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.71
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs17041907; hg19: chr3-16169628;