rs4916319

Positions:

• chr1-173297439-G-A
• chr1-173297439-G-T

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-57416C>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 0.492 in 151,818 control chromosomes in the GnomAD database, including 19,558 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 0.49 (19558 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-57416C>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-90254C>T		intron_variant
TNFSF4	XM_047429902.1	c.19-90254C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74730 AN: 151698 Hom.: 19559 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.492 AC: 74734 AN: 151818 Hom.: 19558 Cov.: 31 AF XY: 0.492 AC XY: 36492 AN XY: 74180

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.512

Alfa AF: 0.550 Hom.: 30230

Bravo AF: 0.480

Asia WGS AF: 0.589 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916319; hg19: chr1-173266578;