rs808276

Variant names:

• chr10-114805628-A-G
• rs808276
• ENST00000729520.1:n.398-12956T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-114805628-A-G
• chr10-114805628-A-T

Variant summary

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

The ENST00000729520.1(ENSG00000295359):​n.398-12956T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,074 control chromosomes in the GnomAD database, including 27,857 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 0.60 (27857 hom., cov: 32)
• Consequence: ENSG00000295359 ENST00000729520.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 3 publications found

Genes affected

ENSG00000295359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902508	XM_047426125.1	c.*224-5185T>C		intron_variant	Intron 1 of 1		XP_047282081.1
LOC124902508	XM_047426127.1	c.*224-7212T>C		intron_variant	Intron 1 of 1		XP_047282083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295359	ENST00000729520.1	n.398-12956T>C		intron_variant	Intron 1 of 1
ENSG00000295359	ENST00000729521.1	n.485-12956T>C		intron_variant	Intron 2 of 2
ENSG00000295359	ENST00000729522.1	n.429-12956T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91556 AN: 151956 Hom.: 27820 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.603 AC: 91661 AN: 152074 Hom.: 27857 Cov.: 32 AF XY: 0.597 AC XY: 44357 AN XY: 74324

African (AFR) AF: 0.670 AC: 27770 AN: 41466

American (AMR) AF: 0.560 AC: 8554 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2082 AN: 3462

East Asian (EAS) AF: 0.441 AC: 2279 AN: 5168

South Asian (SAS) AF: 0.596 AC: 2873 AN: 4824

European-Finnish (FIN) AF: 0.551 AC: 5830 AN: 10578

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40202 AN: 67984

Other (OTH) AF: 0.597 AC: 1263 AN: 2116

Alfa AF: 0.595 Hom.: 21595

Bravo AF: 0.610

Asia WGS AF: 0.568 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.65
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs808276; hg19: chr10-116565387;