rs10804287

Positions:

• chr2-220281744-G-A
• chr2-220281744-G-T

Variant summary

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

The ENST00000432993.1(ENSG00000239498):​n.307-40357G>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 0.213 in 152,110 control chromosomes in the GnomAD database, including 3,784 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 0.21 (3784 hom., cov: 32)
• Consequence: ENST00000432993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.274-40357G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000432993.1	n.307-40357G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32375 AN: 151992 Hom.: 3781 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.213 AC: 32394 AN: 152110 Hom.: 3784 Cov.: 32 AF XY: 0.216 AC XY: 16079 AN XY: 74360

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.234

Alfa AF: 0.233 Hom.: 5815

Bravo AF: 0.207

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10804287; hg19: chr2-221146465;