rs17049741

Variant names:

• chr4-137661557-G-A
• rs17049741
• NR_187911.1:n.140-13098C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-137661557-G-A
• chr4-137661557-G-T

Variant summary

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

The NR_187911.1(LOC101927414):​n.140-13098C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,176 control chromosomes in the GnomAD database, including 2,480 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 0.16 (2480 hom., cov: 32)
• Consequence: LOC101927414 NR_187911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC101927414 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927414	NR_187911.1	n.140-13098C>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23766 AN: 151058 Hom.: 2476 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.157 AC: 23771 AN: 151176 Hom.: 2480 Cov.: 32 AF XY: 0.158 AC XY: 11707 AN XY: 73960

Gnomad4 AFR AF: 0.0388

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.153

Alfa AF: 0.178 Hom.: 2971

Bravo AF: 0.145

Asia WGS AF: 0.309 AC: 1071 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.013
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17049741; hg19: chr4-138582711;