11-7874329-G-T

Variant names:

• chr11-7874329-G-T
• rs10500702
• ENST00000527565.1:n.542+4678C>A

Variant summary

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

The ENST00000527847.5(ENSG00000254951):​n.848+4678C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0889 in 152,026 control chromosomes in the GnomAD database, including 742 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 0.089 (742 hom., cov: 32)
• Consequence: ENSG00000254951 ENST00000527847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 4 publications found

Genes affected

ENSG00000271758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527847.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC283299	NR_036678.1		n.848+4678C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271758	ENST00000527565.1	TSL:3	n.542+4678C>A		intron	N/A
	ENSG00000254951	ENST00000527847.5	TSL:2	n.848+4678C>A		intron	N/A
	ENSG00000254951	ENST00000529488.5	TSL:5	n.531+4678C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13490 AN: 151908 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0889 AC: 13513 AN: 152026 Hom.: 742 Cov.: 32 AF XY: 0.0898 AC XY: 6675 AN XY: 74318

African (AFR) AF: 0.120 AC: 4985 AN: 41528

American (AMR) AF: 0.0727 AC: 1109 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1258 AN: 5164

South Asian (SAS) AF: 0.141 AC: 682 AN: 4824

European-Finnish (FIN) AF: 0.0419 AC: 444 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4402 AN: 67890

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.0744 Hom.: 2148

Bravo AF: 0.0924

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs10500702; hg19: chr11-7895876;