rs844644

Positions:

• chr1-173240356-A-C
• chr1-173240356-A-G

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-333T>G 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 0.617 in 151,922 control chromosomes in the GnomAD database, including 30,478 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 0.62 (30478 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-333T>G		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-33171T>G		intron_variant
TNFSF4	XM_047429902.1	c.19-33171T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93639 AN: 151804 Hom.: 30426 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.617 AC: 93753 AN: 151922 Hom.: 30478 Cov.: 31 AF XY: 0.617 AC XY: 45785 AN XY: 74214

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.620

Alfa AF: 0.541 Hom.: 47201

Bravo AF: 0.638

Asia WGS AF: 0.506 AC: 1756 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
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: rs844644; hg19: chr1-173209495;