rs7009110

chr8-80379644-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000656157.1(ENSG00000253238):n.273+90642T>C 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 0.528 in 152,080 control chromosomes in the GnomAD database, including 22,368 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 0.53 (22368 hom., cov: 32)
• Consequence: ENST00000656157.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 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+90642T>C		intron_variant, non_coding_transcript_variant
	ENST00000644465.1	n.254-69053T>C		intron_variant, non_coding_transcript_variant
	ENST00000656811.1	n.252-23092T>C		intron_variant, non_coding_transcript_variant
	ENST00000662273.1	n.370+90642T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80219 AN: 151962 Hom.: 22370 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.528 AC: 80235 AN: 152080 Hom.: 22368 Cov.: 32 AF XY: 0.529 AC XY: 39296 AN XY: 74344

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.542

Alfa AF: 0.556 Hom.: 3141

Bravo AF: 0.507

Asia WGS AF: 0.505 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	16
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7009110; hg19: chr8-81291879;