rs2162440

Positions:

• chr18-37634043-A-G
• chr18-37634043-A-T

Variant summary

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

The ENST00000649194.1(ENSG00000285940):​n.110+68653A>G 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 0.727 in 151,916 control chromosomes in the GnomAD database, including 41,500 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 0.73 (41500 hom., cov: 30)
• Consequence: ENST00000649194.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 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
	ENST00000649194.1	n.110+68653A>G		intron_variant, non_coding_transcript_variant
	ENST00000661428.1	n.263-3295A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110424 AN: 151800 Hom.: 41482 Cov.: 30

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.727 AC: 110486 AN: 151916 Hom.: 41500 Cov.: 30 AF XY: 0.728 AC XY: 54014 AN XY: 74244

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.765

Alfa AF: 0.794 Hom.: 82530

Bravo AF: 0.717

Asia WGS AF: 0.673 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.47
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2162440; hg19: chr18-35214006;