rs10051722

Positions:

• chr5-130768383-A-C
• chr5-130768383-A-G
• chr5-130768383-A-T

Variant summary

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

The ENST00000661392.1(ENSG00000287390):​n.348+30156T>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 0.34 in 152,028 control chromosomes in the GnomAD database, including 8,974 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 0.34 (8974 hom., cov: 32)
• Consequence: ENST00000661392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661392.1	n.348+30156T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51622 AN: 151910 Hom.: 8947 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.340 AC: 51702 AN: 152028 Hom.: 8974 Cov.: 32 AF XY: 0.346 AC XY: 25702 AN XY: 74328

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.335

Alfa AF: 0.318 Hom.: 4403

Bravo AF: 0.342

Asia WGS AF: 0.453 AC: 1575 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10051722; hg19: chr5-130104076;