rs11997272

Variant names:

• chr8-38701844-C-A
• rs11997272
• ENST00000670774.1:n.53G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-38701844-C-A
• chr8-38701844-C-T

Variant summary

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

The ENST00000670774.1(ENSG00000254321):​n.53G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,198 control chromosomes in the GnomAD database, including 1,913 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 0.14 (1913 hom., cov: 32)
• Consequence: ENSG00000254321 ENST00000670774.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 3 publications found

Genes affected

ENSG00000254321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670774.1. 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
	ENSG00000254321	ENST00000670774.1		n.53G>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000254321	ENST00000521511.1	TSL:3	n.246-228G>T		intron	N/A
	ENSG00000254321	ENST00000811020.1		n.-247G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21300 AN: 152080 Hom.: 1914 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.140 AC: 21312 AN: 152198 Hom.: 1913 Cov.: 32 AF XY: 0.144 AC XY: 10716 AN XY: 74416

African (AFR) AF: 0.117 AC: 4851 AN: 41530

American (AMR) AF: 0.169 AC: 2591 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2519 AN: 5168

South Asian (SAS) AF: 0.114 AC: 553 AN: 4830

European-Finnish (FIN) AF: 0.168 AC: 1782 AN: 10584

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8363 AN: 68002

Other (OTH) AF: 0.131 AC: 277 AN: 2110

Alfa AF: 0.115 Hom.: 1914

Bravo AF: 0.140

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11997272; hg19: chr8-38559362;