chr1-173269597-G-T

Position:

• chr1-173269597-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.656-29574C>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 0.237 in 152,028 control chromosomes in the GnomAD database, including 4,380 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 0.24 (4380 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-29574C>A		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-62412C>A		intron_variant
TNFSF4	XM_047429902.1	c.19-62412C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36080 AN: 151910 Hom.: 4374 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.237 AC: 36104 AN: 152028 Hom.: 4380 Cov.: 32 AF XY: 0.238 AC XY: 17681 AN XY: 74308

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.230

Alfa AF: 0.236 Hom.: 748

Bravo AF: 0.248

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.79
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2022449; hg19: chr1-173238736;