rs7031048

Variant names:

• chr9-21306319-A-G
• rs7031048
• ENST00000778316.1:n.385-30302A>G

Variant summary

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

The ENST00000778316.1(ENSG00000301340):​n.385-30302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,950 control chromosomes in the GnomAD database, including 4,808 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 0.24 (4808 hom., cov: 31)
• Consequence: ENSG00000301340 ENST00000778316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 10 publications found

Genes affected

ENSG00000301340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987053	XR_001746634.2	n.472-30302A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301340	ENST00000778316.1	n.385-30302A>G		intron_variant	Intron 2 of 2
ENSG00000301340	ENST00000778317.1	n.539-30302A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35769 AN: 151832 Hom.: 4803 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.236 AC: 35816 AN: 151950 Hom.: 4808 Cov.: 31 AF XY: 0.237 AC XY: 17634 AN XY: 74288

African (AFR) AF: 0.322 AC: 13323 AN: 41410

American (AMR) AF: 0.282 AC: 4304 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5162

South Asian (SAS) AF: 0.157 AC: 756 AN: 4824

European-Finnish (FIN) AF: 0.194 AC: 2044 AN: 10544

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11571 AN: 67970

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.182 Hom.: 4634

Bravo AF: 0.249

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.67
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7031048; hg19: chr9-21306318;