rs9964595

chr18-1807673-G-A

Variant summary

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

The ENST00000661994.1(ENSG00000266602):n.375-64133G>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 0.409 in 151,786 control chromosomes in the GnomAD database, including 12,984 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 0.41 (12984 hom., cov: 32)
• Consequence: ENST00000661994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 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
	ENST00000661994.1	n.375-64133G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 61997 AN: 151666 Hom.: 12964 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.409 AC: 62064 AN: 151786 Hom.: 12984 Cov.: 32 AF XY: 0.413 AC XY: 30642 AN XY: 74176

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.428

Alfa AF: 0.399 Hom.: 1519

Bravo AF: 0.410

Asia WGS AF: 0.522 AC: 1809 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.49
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9964595; hg19: chr18-1807674;