rs3828570

Positions:

• chr5-601532-G-A
• chr5-601532-G-C
• chr5-601532-G-T

Variant summary

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

The XR_007058672.1(LOC105374608):​n.572+22G>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 0.61 in 152,066 control chromosomes in the GnomAD database, including 28,447 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 0.61 (28447 hom., cov: 32)
• Consequence: LOC105374608 XR_007058672.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

LOC105374608 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374608	XR_007058672.1	n.572+22G>A		intron_variant, non_coding_transcript_variant
LOC105374608	XR_007058673.1	n.244+22G>A		intron_variant, non_coding_transcript_variant
LOC105374608	XR_007058674.1	n.244+22G>A		intron_variant, non_coding_transcript_variant
LOC105374608	XR_007058675.1	n.244+22G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92605 AN: 151948 Hom.: 28413 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.610 AC: 92692 AN: 152066 Hom.: 28447 Cov.: 32 AF XY: 0.610 AC XY: 45317 AN XY: 74332

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.604

Alfa AF: 0.540 Hom.: 2076

Bravo AF: 0.599

Asia WGS AF: 0.473 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3828570; hg19: chr5-601647;