rs1331216

Variant names:

• chr9-94005440-G-A
• rs1331216
• ENST00000766742.1:n.379+24891C>T

Variant summary

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

The ENST00000766742.1(ENSG00000299845):​n.379+24891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,130 control chromosomes in the GnomAD database, including 25,993 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 0.58 (25993 hom., cov: 33)
• Consequence: ENSG00000299845 ENST00000766742.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 publications found

Genes affected

ENSG00000299845 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299845	ENST00000766742.1	n.379+24891C>T		intron_variant	Intron 1 of 1
ENSG00000299845	ENST00000766743.1	n.507+10901C>T		intron_variant	Intron 2 of 2
ENSG00000299845	ENST00000766744.1	n.352-6424C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87860 AN: 152012 Hom.: 25965 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.578 AC: 87940 AN: 152130 Hom.: 25993 Cov.: 33 AF XY: 0.582 AC XY: 43270 AN XY: 74372

African (AFR) AF: 0.658 AC: 27323 AN: 41508

American (AMR) AF: 0.694 AC: 10602 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3466

East Asian (EAS) AF: 0.648 AC: 3349 AN: 5168

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4816

European-Finnish (FIN) AF: 0.579 AC: 6138 AN: 10592

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34614 AN: 67980

Other (OTH) AF: 0.600 AC: 1267 AN: 2112

Alfa AF: 0.551 Hom.: 3048

Bravo AF: 0.595

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1331216; hg19: chr9-96767722;