rs10791740

Variant names:

• chr11-104938927-C-T
• rs10791740
• ENST00000797905.1:n.565+32980C>T

Variant summary

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

The ENST00000797905.1(ENSG00000303891):​n.565+32980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,872 control chromosomes in the GnomAD database, including 8,548 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 0.33 (8548 hom., cov: 32)
• Consequence: ENSG00000303891 ENST00000797905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 6 publications found

Genes affected

ENSG00000303891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797905.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303891	ENST00000797905.1		n.565+32980C>T		intron	N/A
	ENSG00000303891	ENST00000797906.1		n.513-8561C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49748 AN: 151754 Hom.: 8536 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.328 AC: 49821 AN: 151872 Hom.: 8548 Cov.: 32 AF XY: 0.329 AC XY: 24445 AN XY: 74242

African (AFR) AF: 0.421 AC: 17464 AN: 41444

American (AMR) AF: 0.326 AC: 4962 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 813 AN: 3464

East Asian (EAS) AF: 0.188 AC: 969 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4822

European-Finnish (FIN) AF: 0.349 AC: 3691 AN: 10564

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19309 AN: 67866

Other (OTH) AF: 0.343 AC: 725 AN: 2114

Alfa AF: 0.299 Hom.: 11588

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10791740; hg19: chr11-104809654;