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 ENST00000503504.2(ENSG00000254186):​n.513-35400T>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 ENST00000503504.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1374-35400T>A		intron_variant	Intron 2 of 2
LOC105377700	XR_002956233.2	n.1426-35400T>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.2	n.513-35400T>A		intron_variant	Intron 4 of 4	5
ENSG00000254186	ENST00000509211.2	n.528-35400T>A		intron_variant	Intron 4 of 5	3
ENSG00000254186	ENST00000646617.1	n.323-35400T>A		intron_variant	Intron 3 of 14

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 v4.3

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

Other links and lift over

dbSNP: rs7712007; hg19: chr5-162551752;