rs1367272

Positions:

• chr2-7421755-C-T

Variant summary

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

The NR_038432.1(LOC100506274):​n.127+368C>T 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 0.812 in 152,138 control chromosomes in the GnomAD database, including 50,568 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 0.81 (50563 hom., cov: 31)
  • Exomes 𝑓: 0.92 (5 hom.)
• Consequence: LOC100506274 NR_038432.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

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 = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506274	NR_038432.1	n.127+368C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654090.1	n.1477+368C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123459 AN: 152008 Hom.: 50523 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.917 AC: 11 AN: 12 Hom.: 5 Cov.: 0 AF XY: 0.900 AC XY: 9 AN XY: 10

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.812 AC: 123555 AN: 152126 Hom.: 50563 Cov.: 31 AF XY: 0.810 AC XY: 60199 AN XY: 74362

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.826

Alfa AF: 0.831 Hom.: 72974

Bravo AF: 0.812

Asia WGS AF: 0.635 AC: 2209 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	2.0
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367272; hg19: chr2-7561886;