rs10803574

Positions:

• chr2-138953293-G-A

Variant summary

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

The ENST00000656547.1(ENSG00000287147):​n.208-21349G>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 0.343 in 151,844 control chromosomes in the GnomAD database, including 10,318 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 (10318 hom., cov: 32)
• Consequence: ENST00000656547.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

Genes affected

(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 = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373640	XR_923371.2	n.187-21349G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656547.1	n.208-21349G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52152 AN: 151726 Hom.: 10314 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.343 AC: 52155 AN: 151844 Hom.: 10318 Cov.: 32 AF XY: 0.343 AC XY: 25428 AN XY: 74218

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.338

Alfa AF: 0.411 Hom.: 6309

Bravo AF: 0.328

Asia WGS AF: 0.268 AC: 931 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10803574; hg19: chr2-139710863;