rs11006464

Variant names:

• chr10-59386824-T-C
• rs11006464
• ENST00000796729.1:n.*195A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-59386824-T-C
• chr10-59386824-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000796729.1(ENSG00000303721):​n.*195A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 152,132 control chromosomes in the GnomAD database, including 22 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 0.014 (22 hom., cov: 32)
• Consequence: ENSG00000303721 ENST00000796729.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 4 publications found

Genes affected

ENSG00000303721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0136 (2074/152132) while in subpopulation NFE AF = 0.0213 (1448/67958). AF 95% confidence interval is 0.0204. There are 22 homozygotes in GnomAd4. There are 968 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 22 gene

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
ENSG00000303721	ENST00000796729.1	n.*195A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2078 AN: 152014 Hom.: 22 Cov.: 32

Gnomad AFR AF: 0.00437

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0136 AC: 2074 AN: 152132 Hom.: 22 Cov.: 32 AF XY: 0.0130 AC XY: 968 AN XY: 74368

African (AFR) AF: 0.00436 AC: 181 AN: 41534

American (AMR) AF: 0.0168 AC: 257 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4830

European-Finnish (FIN) AF: 0.00301 AC: 32 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1448 AN: 67958

Other (OTH) AF: 0.0241 AC: 51 AN: 2112

Alfa AF: 0.0186 Hom.: 43

Bravo AF: 0.0148

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11006464; hg19: chr10-61146582;