rs10505214

Variant names:

• chr8-114273753-G-C
• rs10505214
• ENST00000777001.1:n.224-3017C>G

Variant summary

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

The ENST00000777001.1(ENSG00000301205):​n.224-3017C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 152,268 control chromosomes in the GnomAD database, including 243 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 0.056 (243 hom., cov: 32)
• Consequence: ENSG00000301205 ENST00000777001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 1 publications found

Genes affected

ENSG00000301205 (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 (NFE) allele frequency at 95% confidence interval = 0.0662 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
ENSG00000301205	ENST00000777001.1	n.224-3017C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8534 AN: 152150 Hom.: 244 Cov.: 32

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0561 AC: 8538 AN: 152268 Hom.: 243 Cov.: 32 AF XY: 0.0537 AC XY: 4002 AN XY: 74462

African (AFR) AF: 0.0473 AC: 1964 AN: 41558

American (AMR) AF: 0.0452 AC: 691 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3472

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5188

South Asian (SAS) AF: 0.0613 AC: 296 AN: 4826

European-Finnish (FIN) AF: 0.0402 AC: 427 AN: 10610

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4612 AN: 68010

Other (OTH) AF: 0.0588 AC: 124 AN: 2108

Alfa AF: 0.0557 Hom.: 28

Bravo AF: 0.0564

Asia WGS AF: 0.0470 AC: 164 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	7.2
DANN	Benign	0.62
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10505214; hg19: chr8-115285982;