rs13271711

Variant names:

• chr8-48451619-C-T
• rs13271711
• ENST00000767280.1:n.425+27104C>T

Variant summary

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

The ENST00000767280.1(ENSG00000299897):​n.425+27104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 125,116 control chromosomes in the GnomAD database, including 132 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 0.040 (132 hom., cov: 30)
• Consequence: ENSG00000299897 ENST00000767280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 2 publications found

Genes affected

ENSG00000299897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299897	ENST00000767280.1		n.425+27104C>T		intron	N/A
	ENSG00000299897	ENST00000767281.1		n.457-21879C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0396 AC: 4956 AN: 125066 Hom.: 133 Cov.: 30

Gnomad AFR AF: 0.00986

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.00107

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0913

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0453

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

GnomAD4 genome AF: 0.0396 AC: 4952 AN: 125116 Hom.: 132 Cov.: 30 AF XY: 0.0415 AC XY: 2422 AN XY: 58368

African (AFR) AF: 0.00984 AC: 322 AN: 32714

American (AMR) AF: 0.0431 AC: 425 AN: 9866

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 227 AN: 3314

East Asian (EAS) AF: 0.00108 AC: 4 AN: 3720

South Asian (SAS) AF: 0.0807 AC: 301 AN: 3732

European-Finnish (FIN) AF: 0.0781 AC: 432 AN: 5530

Middle Eastern (MID) AF: 0.0900 AC: 18 AN: 200

European-Non Finnish (NFE) AF: 0.0481 AC: 3053 AN: 63434

Other (OTH) AF: 0.0446 AC: 77 AN: 1726

Alfa AF: 0.0395 Hom.: 13

Bravo AF: 0.0303

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.43
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13271711; hg19: chr8-49364179;