5-103389394-G-A

Variant names:

• chr5-103389394-G-A
• rs9327881
• ENST00000737662.1:n.35+42707G>A

Variant summary

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

The ENST00000737662.1(ENSG00000296261):​n.35+42707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,046 control chromosomes in the GnomAD database, including 1,447 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 0.12 (1447 hom., cov: 32)
• Consequence: ENSG00000296261 ENST00000737662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 publications found

Genes affected

ENSG00000296261 (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 (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737662.1. 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
	ENSG00000296261	ENST00000737662.1		n.35+42707G>A		intron	N/A
	ENSG00000296261	ENST00000737663.1		n.429+35155G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18658 AN: 151928 Hom.: 1445 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0587

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.123 AC: 18676 AN: 152046 Hom.: 1447 Cov.: 32 AF XY: 0.122 AC XY: 9077 AN XY: 74344

African (AFR) AF: 0.222 AC: 9195 AN: 41452

American (AMR) AF: 0.0727 AC: 1110 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3468

East Asian (EAS) AF: 0.103 AC: 533 AN: 5158

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4818

European-Finnish (FIN) AF: 0.103 AC: 1087 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5844 AN: 67980

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.0997 Hom.: 2442

Bravo AF: 0.128

Asia WGS AF: 0.0860 AC: 303 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	0.026
DANN	Benign	0.29
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9327881; hg19: chr5-102725095;