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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723803	XR_002956872.2	n.356+36549T>G		intron_variant	Intron 3 of 7
LOC102723803	XR_929415.3	n.356+36549T>G		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306944	ENST00000822116.1	n.622+14385T>G		intron_variant	Intron 6 of 6
ENSG00000306944	ENST00000822117.1	n.453+14385T>G		intron_variant	Intron 5 of 5
ENSG00000306944	ENST00000822118.1	n.408+14385T>G		intron_variant	Intron 4 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs7037591; hg19: chr9-1347581;