5-30720171-A-G

Variant names:

• chr5-30720171-A-G
• rs1036475
• ENST00000716668.1:n.129-6708T>C

Variant summary

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

The ENST00000716668.1(ENSG00000287940):​n.129-6708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 152,072 control chromosomes in the GnomAD database, including 68,091 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 0.95 (68091 hom., cov: 33)
• Consequence: ENSG00000287940 ENST00000716668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 1 publications found

Genes affected

ENSG00000287940 (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 (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716668.1. 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
	ENSG00000287940	ENST00000716668.1		n.129-6708T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143769 AN: 151954 Hom.: 68036 Cov.: 33

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.946 AC: 143883 AN: 152072 Hom.: 68091 Cov.: 33 AF XY: 0.947 AC XY: 70367 AN XY: 74324

African (AFR) AF: 0.941 AC: 39064 AN: 41530

American (AMR) AF: 0.970 AC: 14801 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3250 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5014 AN: 5138

South Asian (SAS) AF: 0.975 AC: 4704 AN: 4826

European-Finnish (FIN) AF: 0.908 AC: 9629 AN: 10600

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64302 AN: 67936

Other (OTH) AF: 0.943 AC: 1992 AN: 2112

Alfa AF: 0.923 Hom.: 3861

Bravo AF: 0.951

Asia WGS AF: 0.970 AC: 3372 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	4.6
DANN	Benign	0.70
PhyloP100		0.61

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: rs1036475;

hg19: chr5-30720278;