chr11-7754315-C-T

Variant names:

• chr11-7754315-C-T
• rs722183
• ENST00000527565.1:n.543-49641G>A

Variant summary

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

The ENST00000527565.1(ENSG00000271758):​n.543-49641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,112 control chromosomes in the GnomAD database, including 4,025 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 0.18 (4025 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000271758 ENST00000527565.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527565.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271758	ENST00000527565.1	TSL:3	n.543-49641G>A		intron	N/A
	ENSG00000254951	ENST00000529488.5	TSL:5	n.*78G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27076 AN: 151994 Hom.: 3995 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0697

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.158

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.179 AC: 27155 AN: 152112 Hom.: 4025 Cov.: 32 AF XY: 0.177 AC XY: 13194 AN XY: 74364

African (AFR) AF: 0.403 AC: 16682 AN: 41432

American (AMR) AF: 0.0974 AC: 1489 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.179 AC: 926 AN: 5180

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4808

European-Finnish (FIN) AF: 0.0697 AC: 739 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5234 AN: 68012

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.115 Hom.: 831

Bravo AF: 0.190

Asia WGS AF: 0.223 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.20
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs722183; hg19: chr11-7775862;