rs7001277

Positions:

• chr8-73053924-A-G
• chr8-73053924-A-T

Variant summary

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

The ENST00000517664.1(ENSG00000253636):​n.1747A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,098 control chromosomes in the GnomAD database, including 26,427 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 (26427 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000253636 ENST00000517664.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

Genes affected

ENSG00000253636 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73053924A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253636	ENST00000517664.1	n.1747A>G		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87015 AN: 151980 Hom.: 26433 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.601

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.572 AC: 87048 AN: 152098 Hom.: 26427 Cov.: 32 AF XY: 0.569 AC XY: 42283 AN XY: 74352

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.600

Alfa AF: 0.587 Hom.: 5325

Bravo AF: 0.550

Asia WGS AF: 0.465 AC: 1616 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001277; hg19: chr8-73966159;