rs775800

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373587	XR_923264.2	n.1030-1064T>C		intron_variant	Intron 3 of 4
LOC105373587	XR_923265.2	n.230-1064T>C		intron_variant	Intron 2 of 3
LOC105373587	XR_923266.2	n.1030-1131T>C		intron_variant	Intron 3 of 4
LOC105373587	XR_923267.2	n.202-1064T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302305	ENST00000785655.1	n.277-1064T>C		intron_variant	Intron 2 of 3
ENSG00000302305	ENST00000785656.1	n.231-1131T>C		intron_variant	Intron 2 of 3
ENSG00000302305	ENST00000785657.1	n.230-1131T>C		intron_variant	Intron 2 of 3

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 v4.3

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;