rs16845722

Positions:

• chr1-173358366-G-A
• chr1-173358366-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.655+103958C>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 0.0986 in 152,154 control chromosomes in the GnomAD database, including 864 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 0.099 (864 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• 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.655+103958C>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.147+83553C>T		intron_variant
TNFSF4	XM_047429902.1	c.18+43893C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14960 AN: 152036 Hom.: 859 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0986 AC: 15008 AN: 152154 Hom.: 864 Cov.: 32 AF XY: 0.101 AC XY: 7502 AN XY: 74362

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0587 Hom.: 81

Bravo AF: 0.0958

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.79
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16845722; hg19: chr1-173327505;