rs1265750

Positions:

• chr2-80724698-T-C
• chr2-80724698-T-G

Variant summary

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

The ENST00000450290.1(ENSG00000230975):​n.469-21004A>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 0.712 in 152,136 control chromosomes in the GnomAD database, including 41,349 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 0.71 (41349 hom., cov: 32)
• Consequence: ENST00000450290.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450290.1	n.469-21004A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108291 AN: 152018 Hom.: 41345 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.712 AC: 108333 AN: 152136 Hom.: 41349 Cov.: 32 AF XY: 0.713 AC XY: 53024 AN XY: 74382

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.734

Alfa AF: 0.811 Hom.: 60841

Bravo AF: 0.695

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1265750; hg19: chr2-80951823;