rs7702331

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513280.3. 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
	ENSG00000249743	ENST00000513280.3	TSL:3	n.320-31180A>G		intron	N/A
	ENSG00000249743	ENST00000513379.1	TSL:5	n.329-31180A>G		intron	N/A
	ENSG00000249743	ENST00000515556.7	TSL:3	n.438-31180A>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs7702331;

hg19: chr5-72551134;