chr5-73255307-A-G

Variant names:

• chr5-73255307-A-G
• rs7702331
• ENST00000513280.3:n.320-31180A>G

Variant summary

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

The ENST00000513280.3(ENSG00000249743):​n.320-31180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,818 control chromosomes in the GnomAD database, including 13,319 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 0.41 (13319 hom., cov: 31)
• Consequence: ENSG00000249743 ENST00000513280.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 52 publications found

Genes affected

ENSG00000249743 (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 (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901002	XR_007058818.1	n.347-31180A>G		intron_variant	Intron 1 of 2
LOC105379031	XR_948470.3	n.246-8651T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249743	ENST00000513280.3	n.320-31180A>G		intron_variant	Intron 1 of 5	3
ENSG00000249743	ENST00000513379.1	n.329-31180A>G		intron_variant	Intron 1 of 4	5
ENSG00000249743	ENST00000515556.7	n.438-31180A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62022 AN: 151700 Hom.: 13295 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.409 AC: 62095 AN: 151818 Hom.: 13319 Cov.: 31 AF XY: 0.404 AC XY: 29942 AN XY: 74180

African (AFR) AF: 0.528 AC: 21822 AN: 41346

American (AMR) AF: 0.345 AC: 5263 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3468

East Asian (EAS) AF: 0.156 AC: 805 AN: 5166

South Asian (SAS) AF: 0.275 AC: 1314 AN: 4784

European-Finnish (FIN) AF: 0.364 AC: 3831 AN: 10534

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26546 AN: 67944

Other (OTH) AF: 0.404 AC: 854 AN: 2116

Alfa AF: 0.391 Hom.: 55916

Bravo AF: 0.412

Asia WGS AF: 0.210 AC: 731 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	0.83
DANN	Benign	0.37
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7702331; hg19: chr5-72551134;