rs2006970

chr4-43318490-C-A

Variant summary

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

The XR_925266.3(LOC105374433):n.202+2209C>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 0.518 in 152,074 control chromosomes in the GnomAD database, including 22,002 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 0.52 (22002 hom., cov: 34)
• Consequence: LOC105374433 XR_925266.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

LOC105374433 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374433	XR_925266.3	n.202+2209C>A		intron_variant, non_coding_transcript_variant
LOC105374434	XR_925268.1	n.144-10452G>T		intron_variant, non_coding_transcript_variant
LOC105374433	XR_925267.3	n.202+2209C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78802 AN: 151956 Hom.: 22009 Cov.: 34

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.518 AC: 78801 AN: 152074 Hom.: 22002 Cov.: 34 AF XY: 0.509 AC XY: 37862 AN XY: 74338

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.533

Alfa AF: 0.582 Hom.: 3352

Bravo AF: 0.508

Asia WGS AF: 0.314 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2006970; hg19: chr4-43320507;