rs6992476

Positions:

• chr8-80355471-A-G

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.273+66469A>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 0.575 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: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656157.1	n.273+66469A>G		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.253+66469A>G		intron_variant, non_coding_transcript_variant
	ENST00000656811.1	n.252-47265A>G		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.370+66469A>G		intron_variant, non_coding_transcript_variant

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;