rs491222

Positions:

• chr18-2089891-G-A
• chr18-2089891-G-C

Variant summary

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

The ENST00000639316.2(ENSG00000263745):​n.619+36309C>T 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 0.527 in 151,954 control chromosomes in the GnomAD database, including 21,927 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 0.53 (21927 hom., cov: 32)
• Consequence: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371956	XR_935087.3	n.271+21753C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639316.2	n.619+36309C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79966 AN: 151836 Hom.: 21906 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.527 AC: 80025 AN: 151954 Hom.: 21927 Cov.: 32 AF XY: 0.531 AC XY: 39472 AN XY: 74268

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.532

Alfa AF: 0.452 Hom.: 15565

Bravo AF: 0.541

Asia WGS AF: 0.667 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs491222; hg19: chr18-2089892;