rs627953

Positions:

• chr18-10121952-G-A
• chr18-10121952-G-C
• chr18-10121952-G-T

Variant summary

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

The ENST00000685786.1(ENSG00000265554):​n.389-22205G>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 0.363 in 152,136 control chromosomes in the GnomAD database, including 11,323 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 0.36 (11323 hom., cov: 33)
• Consequence: ENST00000685786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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
	ENST00000685786.1	n.389-22205G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55112 AN: 152018 Hom.: 11299 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.363 AC: 55188 AN: 152136 Hom.: 11323 Cov.: 33 AF XY: 0.368 AC XY: 27385 AN XY: 74390

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.354

Alfa AF: 0.276 Hom.: 12340

Bravo AF: 0.377

Asia WGS AF: 0.548 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs627953; hg19: chr18-10121949;