rs11997272

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521511.1(ENSG00000254321):​n.246-228G>T variant causes a intron, non coding transcript 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: ENST00000521511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000521511.1	n.246-228G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000670774.1	n.53G>T		non_coding_transcript_exon_variant	1/3

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.131

Alfa AF: 0.114 Hom.: 1501

Bravo AF: 0.140

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11997272; hg19: chr8-38559362;