rs1564632

Variant names:

• chr11-7895165-C-A
• rs1564632
• ENST00000527847.5:n.353+10438G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-7895165-C-A
• chr11-7895165-C-T

Variant summary

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

The ENST00000527847.5(ENSG00000254951):​n.353+10438G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,042 control chromosomes in the GnomAD database, including 4,382 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 0.23 (4382 hom., cov: 32)
• Consequence: ENSG00000254951 ENST00000527847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 2 publications found

Genes affected

ENSG00000254951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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.353+10438G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254951	ENST00000527847.5	TSL:2	n.353+10438G>T		intron	N/A
	ENSG00000254951	ENST00000718815.1		n.373+10438G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35311 AN: 151926 Hom.: 4371 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.233 AC: 35361 AN: 152042 Hom.: 4382 Cov.: 32 AF XY: 0.236 AC XY: 17511 AN XY: 74314

African (AFR) AF: 0.294 AC: 12185 AN: 41464

American (AMR) AF: 0.235 AC: 3595 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 968 AN: 3462

East Asian (EAS) AF: 0.138 AC: 714 AN: 5182

South Asian (SAS) AF: 0.167 AC: 805 AN: 4812

European-Finnish (FIN) AF: 0.262 AC: 2773 AN: 10564

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13660 AN: 67958

Other (OTH) AF: 0.237 AC: 502 AN: 2114

Alfa AF: 0.201 Hom.: 2245

Bravo AF: 0.237

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1564632;

hg19: chr11-7916712;