rs2204599

Positions:

• chr2-78034277-A-G
• chr2-78034277-A-T

Variant summary

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

The NR_110288.1(LOC101927967):​n.345-159215T>C 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 0.86 in 152,070 control chromosomes in the GnomAD database, including 56,465 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 0.86 (56465 hom., cov: 33)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-159215T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667782.1	n.83-94391T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130713 AN: 151942 Hom.: 56410 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.860 AC: 130832 AN: 152070 Hom.: 56465 Cov.: 33 AF XY: 0.865 AC XY: 64299 AN XY: 74354

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.864

Alfa AF: 0.828 Hom.: 10186

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2204599; hg19: chr2-78261403;