rs4959923

Positions:

• chr6-467773-A-G
• chr6-467773-A-T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-7435A>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 0.863 in 152,116 control chromosomes in the GnomAD database, including 56,842 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 0.86 (56842 hom., cov: 31)
• Consequence: ENST00000661640.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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 (NFE) allele frequency at 95% confidence interval = 0.903 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
	ENST00000661640.1	n.336-7435A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131149 AN: 151998 Hom.: 56808 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.863 AC: 131242 AN: 152116 Hom.: 56842 Cov.: 31 AF XY: 0.860 AC XY: 63935 AN XY: 74360

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.864

Alfa AF: 0.894 Hom.: 78841

Bravo AF: 0.857

Asia WGS AF: 0.798 AC: 2775 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	0.17
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959923; hg19: chr6-467773;