rs606490

chr5-10318343-G-A

Variant summary

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

The XR_925783.3(LOC105374651):n.42-737G>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 0.197 in 152,144 control chromosomes in the GnomAD database, including 3,366 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 0.20 (3366 hom., cov: 31)
• Consequence: LOC105374651 XR_925783.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

Genes affected

LOC105374651 (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 (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374651	XR_925783.3	n.42-737G>A		intron_variant, non_coding_transcript_variant
LOC105374651	XR_925786.3	n.42-737G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29947 AN: 152028 Hom.: 3363 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.197 AC: 29966 AN: 152144 Hom.: 3366 Cov.: 31 AF XY: 0.190 AC XY: 14163 AN XY: 74382

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.201

Alfa AF: 0.174 Hom.: 5043

Bravo AF: 0.200

Asia WGS AF: 0.0710 AC: 248 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	1.5
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs606490; hg19: chr5-10318455;