chr7-94062432-G-A

Variant names:

• chr7-94062432-G-A
• rs9918668
• ENST00000415536.5:n.341+568G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415536.5(BET1-AS1):​n.341+568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,056 control chromosomes in the GnomAD database, including 18,189 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 0.46 (18189 hom., cov: 32)
• Consequence: BET1-AS1 ENST00000415536.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 5 publications found

Genes affected

BET1-AS1 (HGNC:40690): (BET1 antisense RNA 1)

LOC130890646 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415536.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC130890646	NR_186703.1		n.368+568G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BET1-AS1	ENST00000415536.5	TSL:3	n.341+568G>A		intron	N/A
	BET1-AS1	ENST00000438538.2	TSL:3	n.518+568G>A		intron	N/A
	BET1-AS1	ENST00000718187.1		n.612+568G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70599 AN: 151940 Hom.: 18152 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.465 AC: 70686 AN: 152056 Hom.: 18189 Cov.: 32 AF XY: 0.463 AC XY: 34387 AN XY: 74326

African (AFR) AF: 0.682 AC: 28286 AN: 41458

American (AMR) AF: 0.320 AC: 4888 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3468

East Asian (EAS) AF: 0.641 AC: 3310 AN: 5164

South Asian (SAS) AF: 0.360 AC: 1735 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3901 AN: 10566

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25970 AN: 67986

Other (OTH) AF: 0.422 AC: 890 AN: 2108

Alfa AF: 0.418 Hom.: 25592

Bravo AF: 0.469

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.33
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9918668; hg19: chr7-93691744;