chr5-14570623-A-G

Variant names:

• chr5-14570623-A-G
• rs39968
• ENST00000828393.1:n.165+2185T>C

Variant summary

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

The ENST00000828393.1(ENSG00000307738):​n.165+2185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,176 control chromosomes in the GnomAD database, including 38,718 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 0.71 (38718 hom., cov: 33)
• Consequence: ENSG00000307738 ENST00000828393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 4 publications found

Genes affected

ENSG00000307738 (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 (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000828393.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307738	ENST00000828393.1		n.165+2185T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107900 AN: 152058 Hom.: 38673 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.710 AC: 108003 AN: 152176 Hom.: 38718 Cov.: 33 AF XY: 0.706 AC XY: 52522 AN XY: 74398

African (AFR) AF: 0.827 AC: 34338 AN: 41520

American (AMR) AF: 0.636 AC: 9724 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3030 AN: 5176

South Asian (SAS) AF: 0.616 AC: 2974 AN: 4826

European-Finnish (FIN) AF: 0.637 AC: 6742 AN: 10588

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46528 AN: 68000

Other (OTH) AF: 0.711 AC: 1500 AN: 2110

Alfa AF: 0.690 Hom.: 62006

Bravo AF: 0.717

Asia WGS AF: 0.625 AC: 2176 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	0.16
DANN	Benign	0.48
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs39968;

hg19: chr5-14570732;