chr5-117039777-A-G

Variant names:

• chr5-117039777-A-G
• rs930922
• ENST00000736440.1:n.222+8347A>G

Variant summary

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

The ENST00000736440.1(ENSG00000250949):​n.222+8347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,182 control chromosomes in the GnomAD database, including 3,062 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 0.19 (3062 hom., cov: 32)
• Consequence: ENSG00000250949 ENST00000736440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 2 publications found

Genes affected

ENSG00000250949 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736440.1. 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
	ENSG00000250949	ENST00000736440.1		n.222+8347A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29164 AN: 152064 Hom.: 3058 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.192 AC: 29179 AN: 152182 Hom.: 3062 Cov.: 32 AF XY: 0.191 AC XY: 14221 AN XY: 74400

African (AFR) AF: 0.133 AC: 5533 AN: 41526

American (AMR) AF: 0.201 AC: 3073 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 873 AN: 3472

East Asian (EAS) AF: 0.00597 AC: 31 AN: 5192

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4814

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10586

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15815 AN: 67992

Other (OTH) AF: 0.205 AC: 433 AN: 2108

Alfa AF: 0.222 Hom.: 7380

Bravo AF: 0.185

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.69
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs930922; hg19: chr5-116375473;