rs11599710

Positions:

• chr10-100346031-G-A

Variant summary

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

The variant allele was found at a frequency of 0.0905 in 152,092 control chromosomes in the GnomAD database, including 678 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 0.091 (678 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100346031G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231188	ENST00000429420.1	n.103+257C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13763 AN: 151976 Hom.: 680 Cov.: 32

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0905 AC: 13766 AN: 152092 Hom.: 678 Cov.: 32 AF XY: 0.0901 AC XY: 6697 AN XY: 74342

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0893 Hom.: 235

Bravo AF: 0.0889

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11599710; hg19: chr10-102105788;