2-77819666-C-T

Position:

• chr2-77819666-C-T

Variant summary

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

The NR_110288.1(LOC101927967):​n.549+20103G>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 0.408 in 151,918 control chromosomes in the GnomAD database, including 12,739 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 0.41 (12739 hom., cov: 32)
• Consequence: LOC101927967 NR_110288.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.549+20103G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667782.1	n.343+20103G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61880 AN: 151800 Hom.: 12721 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.408 AC: 61944 AN: 151918 Hom.: 12739 Cov.: 32 AF XY: 0.413 AC XY: 30643 AN XY: 74258

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.418

Alfa AF: 0.389 Hom.: 11616

Bravo AF: 0.403

Asia WGS AF: 0.575 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2861215; hg19: chr2-78046792;