1-173364690-G-T

Position:

• chr1-173364690-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.655+97634C>A 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 0.695 in 151,562 control chromosomes in the GnomAD database, including 36,803 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 0.70 (36803 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.655+97634C>A		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.147+77229C>A		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.18+37569C>A		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105274 AN: 151446 Hom.: 36783 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.695 AC: 105339 AN: 151562 Hom.: 36803 Cov.: 31 AF XY: 0.695 AC XY: 51499 AN XY: 74052

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.704

Alfa AF: 0.653 Hom.: 64364

Bravo AF: 0.700

Asia WGS AF: 0.628 AC: 2179 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.88
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916334; hg19: chr1-173333829;