rs6992476

Variant names:

• chr8-80355471-A-G
• rs6992476
• ENST00000644465.1:n.253+66469A>G

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.253+66469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,976 control chromosomes in the GnomAD database, including 25,821 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 0.57 (25821 hom., cov: 32)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 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
ENSG00000253238	ENST00000644465.1	n.253+66469A>G		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656157.1	n.273+66469A>G		intron_variant	Intron 2 of 3
ENSG00000253238	ENST00000656811.1	n.252-47265A>G		intron_variant	Intron 2 of 2
ENSG00000253238	ENST00000662273.1	n.370+66469A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87332 AN: 151858 Hom.: 25823 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.575 AC: 87359 AN: 151976 Hom.: 25821 Cov.: 32 AF XY: 0.574 AC XY: 42667 AN XY: 74302

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.581

Alfa AF: 0.602 Hom.: 10216

Bravo AF: 0.554

Asia WGS AF: 0.508 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6992476; hg19: chr8-81267706;