10-47317214-G-A

Variant names:

• chr10-47317214-G-A
• rs4922505
• ENST00000816238.1:n.*55G>A

Variant summary

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

The ENST00000816238.1(ENSG00000306200):​n.*55G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 152,370 control chromosomes in the GnomAD database, including 71,310 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 0.97 (71310 hom., cov: 35)
• Consequence: ENSG00000306200 ENST00000816238.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 1 publications found

Genes affected

ENSG00000306200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816238.1. 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
	ENSG00000306200	ENST00000816238.1		n.*55G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.967 AC: 147268 AN: 152252 Hom.: 71261 Cov.: 35

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.967 AC: 147376 AN: 152370 Hom.: 71310 Cov.: 35 AF XY: 0.966 AC XY: 71966 AN XY: 74508

African (AFR) AF: 0.951 AC: 39548 AN: 41584

American (AMR) AF: 0.943 AC: 14444 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3394 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4822 AN: 5192

South Asian (SAS) AF: 0.901 AC: 4344 AN: 4820

European-Finnish (FIN) AF: 0.988 AC: 10499 AN: 10626

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67063 AN: 68044

Other (OTH) AF: 0.976 AC: 2066 AN: 2116

Alfa AF: 0.977 Hom.: 107778

Bravo AF: 0.964

Asia WGS AF: 0.922 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.65
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs4922505; hg19: chr10-48422148;