rs7235755

Positions:

• chr18-37636298-A-G

Variant summary

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

The ENST00000649194.1(ENSG00000285940):​n.110+70908A>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 0.755 in 151,920 control chromosomes in the GnomAD database, including 43,978 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 0.76 (43978 hom., cov: 31)
• Consequence: ENST00000649194.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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+70908A>G		intron_variant, non_coding_transcript_variant
	ENST00000661428.1	n.263-1040A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114677 AN: 151802 Hom.: 43956 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.755 AC: 114750 AN: 151920 Hom.: 43978 Cov.: 31 AF XY: 0.755 AC XY: 56044 AN XY: 74216

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.781

Alfa AF: 0.785 Hom.: 21687

Bravo AF: 0.750

Asia WGS AF: 0.677 AC: 2350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7235755; hg19: chr18-35216261;