rs9643449

Positions:

• chr8-82758572-A-G
• chr8-82758572-A-T

Variant summary

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

The ENST00000663058.1(ENSG00000254394):​n.944-154367A>G 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 0.654 in 152,002 control chromosomes in the GnomAD database, including 32,684 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 0.65 (32684 hom., cov: 32)
• Consequence: ENST00000663058.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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
	ENST00000663058.1	n.944-154367A>G		intron_variant, non_coding_transcript_variant
	ENST00000658531.1	n.254-145083A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99231 AN: 151882 Hom.: 32634 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.654 AC: 99339 AN: 152002 Hom.: 32684 Cov.: 32 AF XY: 0.652 AC XY: 48462 AN XY: 74296

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.651

Alfa AF: 0.657 Hom.: 53057

Bravo AF: 0.645

Asia WGS AF: 0.589 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9643449; hg19: chr8-83670807;