rs1342038

Positions:

• chr1-173332377-G-A
• chr1-173332377-G-C

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-92354C>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 0.432 in 151,926 control chromosomes in the GnomAD database, including 14,390 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 0.43 (14390 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

LOC100506023 (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 (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-92354C>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.147+109542C>T		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.18+69882C>T		intron_variant			XP_047285858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65580 AN: 151808 Hom.: 14387 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.432 AC: 65621 AN: 151926 Hom.: 14390 Cov.: 31 AF XY: 0.435 AC XY: 32329 AN XY: 74264

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.427

Alfa AF: 0.410 Hom.: 25505

Bravo AF: 0.441

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342038; hg19: chr1-173301516;