rs7000782

Positions:

• chr8-80395915-T-A

Variant summary

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

The ENST00000656157.1(ENSG00000253238):​n.274-86693T>A 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 0.54 in 150,036 control chromosomes in the GnomAD database, including 23,418 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 0.54 (23418 hom., cov: 26)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 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
	ENST00000656157.1	n.274-86693T>A		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.254-52782T>A		intron_variant, non_coding_transcript_variant
	ENST00000656811.1	n.252-6821T>A		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.371-86693T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.540 AC: 80974 AN: 149924 Hom.: 23371 Cov.: 26

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.540 AC: 81081 AN: 150036 Hom.: 23418 Cov.: 26 AF XY: 0.541 AC XY: 39478 AN XY: 73028

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.491

Alfa AF: 0.493 Hom.: 2419

Bravo AF: 0.561

Asia WGS AF: 0.574 AC: 1997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.36
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7000782; hg19: chr8-81308150;