rs1263663

Variant names:

• chr14-22552827-T-C
• rs1263663

Your query was ambiguous. Multiple possible variants found:

• chr14-22552827-T-C
• chr14-22552827-T-G

Variant summary

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

The variant allele was found at a frequency of 0.464 in 151,920 control chromosomes in the GnomAD database, including 17,289 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 0.46 (17289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70424 AN: 151802 Hom.: 17259 Cov.: 31

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.464 AC: 70512 AN: 151920 Hom.: 17289 Cov.: 31 AF XY: 0.463 AC XY: 34397 AN XY: 74244

African (AFR) AF: 0.627 AC: 25955 AN: 41428

American (AMR) AF: 0.453 AC: 6915 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3468

East Asian (EAS) AF: 0.190 AC: 983 AN: 5168

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 4987 AN: 10528

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27137 AN: 67938

Other (OTH) AF: 0.464 AC: 974 AN: 2100

Alfa AF: 0.417 Hom.: 22551

Bravo AF: 0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.3
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1263663; hg19: chr14-23021770;