rs7037591

Variant names:

• chr9-1347581-T-G
• rs7037591
• ENST00000822116.1:n.622+14385T>G

Variant summary

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

The ENST00000822116.1(ENSG00000306944):​n.622+14385T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,216 control chromosomes in the GnomAD database, including 408 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 0.067 (408 hom., cov: 33)
• Consequence: ENSG00000306944 ENST00000822116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 0 publications found

Genes affected

ENSG00000306944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822116.1. 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
	ENSG00000306944	ENST00000822116.1		n.622+14385T>G		intron	N/A
	ENSG00000306944	ENST00000822117.1		n.453+14385T>G		intron	N/A
	ENSG00000306944	ENST00000822118.1		n.408+14385T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10239 AN: 152098 Hom.: 405 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0673 AC: 10248 AN: 152216 Hom.: 408 Cov.: 33 AF XY: 0.0689 AC XY: 5124 AN XY: 74418

African (AFR) AF: 0.0396 AC: 1648 AN: 41570

American (AMR) AF: 0.0566 AC: 865 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.169 AC: 872 AN: 5154

South Asian (SAS) AF: 0.136 AC: 656 AN: 4822

European-Finnish (FIN) AF: 0.0812 AC: 861 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4747 AN: 68008

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.0712 Hom.: 576

Bravo AF: 0.0645

Asia WGS AF: 0.152 AC: 526 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.3
DANN	Benign	0.67
PhyloP100		0.53

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: rs7037591;

hg19: chr9-1347581;