rs7712007

Variant names:

• chr5-163124746-A-T
• rs7712007
• ENST00000503504.2:n.513-35400T>A

Variant summary

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

The ENST00000509211.2(ENSG00000254186):​n.528-35400T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,268 control chromosomes in the GnomAD database, including 605 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 0.085 (605 hom., cov: 33)
• Consequence: ENSG00000254186 ENST00000509211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 0 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509211.2. 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
	ENSG00000254186	ENST00000503504.2	TSL:5	n.513-35400T>A		intron	N/A
	ENSG00000254186	ENST00000509211.2	TSL:3	n.528-35400T>A		intron	N/A
	ENSG00000254186	ENST00000646617.1		n.323-35400T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12940 AN: 152150 Hom.: 605 Cov.: 33

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.00904

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0850 AC: 12947 AN: 152268 Hom.: 605 Cov.: 33 AF XY: 0.0844 AC XY: 6280 AN XY: 74440

African (AFR) AF: 0.0872 AC: 3626 AN: 41564

American (AMR) AF: 0.0889 AC: 1360 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.00887 AC: 46 AN: 5186

South Asian (SAS) AF: 0.0975 AC: 470 AN: 4820

European-Finnish (FIN) AF: 0.0786 AC: 833 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5989 AN: 68014

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0803 Hom.: 66

Bravo AF: 0.0843

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		-0.21

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: rs7712007;

hg19: chr5-162551752;