rs2861264

Positions:

• chr2-78139951-G-A

Variant summary

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

The NR_110288.1(LOC101927967):​n.344+150437C>T 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 0.0878 in 151,986 control chromosomes in the GnomAD database, including 691 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 0.088 (691 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927967	NR_110288.1	n.344+150437C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667782.1	n.82+150437C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13345 AN: 151868 Hom.: 691 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.0878 AC: 13342 AN: 151986 Hom.: 691 Cov.: 32 AF XY: 0.0895 AC XY: 6647 AN XY: 74274

Gnomad4 AFR AF: 0.0472

Gnomad4 AMR AF: 0.0779

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.0697

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.105 Hom.: 425

Bravo AF: 0.0829

Asia WGS AF: 0.0820 AC: 285 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2861264; hg19: chr2-78367077;