7-110228018-G-T

Variant summary

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

The ENST00000667232.1(ENSG00000226965):n.487-47008C>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 0.61 in 151,908 control chromosomes in the GnomAD database, including 28,636 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 0.61 (28636 hom., cov: 32)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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
	ENST00000667232.1	n.487-47008C>A		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.406-47008C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92563 AN: 151790 Hom.: 28606 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.610 AC: 92643 AN: 151908 Hom.: 28636 Cov.: 32 AF XY: 0.616 AC XY: 45750 AN XY: 74222

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.611

Alfa AF: 0.466 Hom.: 1341

Bravo AF: 0.614

Asia WGS AF: 0.649 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.23
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1013920; hg19: chr7-109868075;