chr2-121055323-T-C

Variant names:

• chr2-121055323-T-C
• rs775800
• ENST00000785655.1:n.277-1064T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000785655.1(ENSG00000302305):​n.277-1064T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,006 control chromosomes in the GnomAD database, including 9,668 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 0.35 (9668 hom., cov: 31)
• Consequence: ENSG00000302305 ENST00000785655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.944
• Publications: 5 publications found

Genes affected

ENSG00000302305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785655.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302305	ENST00000785655.1		n.277-1064T>C		intron	N/A
	ENSG00000302305	ENST00000785656.1		n.231-1131T>C		intron	N/A
	ENSG00000302305	ENST00000785657.1		n.230-1131T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53735 AN: 151888 Hom.: 9657 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.354 AC: 53773 AN: 152006 Hom.: 9668 Cov.: 31 AF XY: 0.360 AC XY: 26722 AN XY: 74288

African (AFR) AF: 0.332 AC: 13769 AN: 41458

American (AMR) AF: 0.379 AC: 5795 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2517 AN: 5148

South Asian (SAS) AF: 0.512 AC: 2466 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3970 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22713 AN: 67958

Other (OTH) AF: 0.356 AC: 751 AN: 2108

Alfa AF: 0.352 Hom.: 5392

Bravo AF: 0.353

Asia WGS AF: 0.491 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.77
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs775800; hg19: chr2-121812899;