rs7780181

Positions:

• chr7-137021788-T-G

Variant summary

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

The NR_046103.1(LOC349160):​n.341+11006A>C 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 0.445 in 151,630 control chromosomes in the GnomAD database, including 15,636 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 0.45 (15636 hom., cov: 31)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+11006A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+11006A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67461 AN: 151512 Hom.: 15603 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.445 AC: 67534 AN: 151630 Hom.: 15636 Cov.: 31 AF XY: 0.438 AC XY: 32457 AN XY: 74078

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.439

Alfa AF: 0.444 Hom.: 9379

Bravo AF: 0.444

Asia WGS AF: 0.219 AC: 764 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780181; hg19: chr7-136706535;