rs9325776

Positions:

• chr8-15960047-G-A
• chr8-15960047-G-C

Variant summary

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

The ENST00000664439.1(ENSG00000287476):​n.163+5298C>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 0.943 in 152,180 control chromosomes in the GnomAD database, including 67,985 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 0.94 (67985 hom., cov: 33)
• Consequence: ENST00000664439.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 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
	ENST00000664439.1	n.163+5298C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143425 AN: 152062 Hom.: 67949 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.943 AC: 143511 AN: 152180 Hom.: 67985 Cov.: 33 AF XY: 0.942 AC XY: 70085 AN XY: 74400

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.952

Alfa AF: 0.946 Hom.: 17960

Bravo AF: 0.930

Asia WGS AF: 0.892 AC: 3098 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9325776; hg19: chr8-15817556;