rs11971309

chr7-137027408-C-T

Variant summary

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

The NR_046103.1(LOC349160):n.341+5386G>A 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 0.302 in 152,002 control chromosomes in the GnomAD database, including 7,766 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 0.30 (7766 hom., cov: 32)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+5386G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+5386G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45907 AN: 151884 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.302 AC: 45932 AN: 152002 Hom.: 7766 Cov.: 32 AF XY: 0.299 AC XY: 22219 AN XY: 74270

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.323

Alfa AF: 0.351 Hom.: 5339

Bravo AF: 0.291

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
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: rs11971309; hg19: chr7-136712155;