rs17506824

chr7-137024766-T-C

Variant summary

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

The NR_046103.1(LOC349160):n.341+8028A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,836 control chromosomes in the GnomAD database, including 26,475 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 0.57 (26475 hom., cov: 32)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+8028A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+8028A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87211 AN: 151718 Hom.: 26443 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.575 AC: 87281 AN: 151836 Hom.: 26475 Cov.: 32 AF XY: 0.568 AC XY: 42167 AN XY: 74178

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.571

Alfa AF: 0.558 Hom.: 12422

Bravo AF: 0.570

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.26
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17506824; hg19: chr7-136709513;