rs10499320

Positions:

• chr7-3093749-G-C

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, non coding transcript 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: ENST00000667422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667422.1	n.76-6360C>G		intron_variant, non_coding_transcript_variant

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;