rs10499320

Variant names:

• chr7-3093749-G-C
• rs10499320
• ENST00000667422.1:n.76-6360C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667422.1(ENSG00000228334):​n.76-6360C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,032 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 31)
• Consequence: ENSG00000228334 ENST00000667422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

ENSG00000228334 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228334	ENST00000667422.1	n.76-6360C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17272 AN: 151914 Hom.: 1088 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.114 AC: 17269 AN: 152032 Hom.: 1090 Cov.: 31 AF XY: 0.112 AC XY: 8319 AN XY: 74314

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.130

Alfa AF: 0.120 Hom.: 149

Bravo AF: 0.112

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499320; hg19: chr7-3133383;