rs17047697

Variant names:

• chr2-118070234-G-A
• rs17047697
• XR_001739662.3:n.182-7218C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739662.3(LOC107985940):​n.182-7218C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,762 control chromosomes in the GnomAD database, including 6,114 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 0.27 (6114 hom., cov: 32)
• Consequence: LOC107985940 XR_001739662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.182-7218C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41053 AN: 151644 Hom.: 6118 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.270 AC: 41051 AN: 151762 Hom.: 6114 Cov.: 32 AF XY: 0.271 AC XY: 20128 AN XY: 74140

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.297

Alfa AF: 0.317 Hom.: 10053

Bravo AF: 0.263

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17047697; hg19: chr2-118827810;