rs10075974

Positions:

• chr5-92444950-A-G

Variant summary

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

The ENST00000507217.5(ENSG00000250049):​n.528+29266A>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 0.0574 in 151,810 control chromosomes in the GnomAD database, including 282 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 0.057 (282 hom., cov: 31)
• Consequence: ENST00000507217.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379080	XR_001742806.2	n.5737+29266A>G		intron_variant, non_coding_transcript_variant
LOC105379080	XR_007058867.1	n.5590+29266A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000507217.5	n.528+29266A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000512210.5	n.406-34589T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000513779.1	n.253-12661T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8716 AN: 151692 Hom.: 284 Cov.: 31

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.0947

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0574 AC: 8710 AN: 151810 Hom.: 282 Cov.: 31 AF XY: 0.0570 AC XY: 4231 AN XY: 74170

Gnomad4 AFR AF: 0.0386

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0718

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.0670

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0670 Hom.: 173

Bravo AF: 0.0542

Asia WGS AF: 0.0440 AC: 154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	10
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: rs10075974; hg19: chr5-91780657;