rs16845685

chr1-173344747-G-A

Variant summary

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

The NR_037845.1(LOC100506023):n.656-104724C>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 0.101 in 152,164 control chromosomes in the GnomAD database, including 915 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 0.10 (915 hom., cov: 33)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

LOC100506023 (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 (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-104724C>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.147+97172C>T		intron_variant
TNFSF4	XM_047429902.1	c.18+57512C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 152046 Hom.: 910 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.101 AC: 15411 AN: 152164 Hom.: 915 Cov.: 33 AF XY: 0.103 AC XY: 7676 AN XY: 74372

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0792

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0784

Alfa AF: 0.0949 Hom.: 127

Bravo AF: 0.0990

Asia WGS AF: 0.222 AC: 770 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.99
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16845685; hg19: chr1-173313886;