rs7244227

Positions:

• chr18-51023575-A-G
• chr18-51023575-A-T

Variant summary

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

The ENST00000701227.1(ENSG00000289868):​n.134-3950T>C 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 0.351 in 152,088 control chromosomes in the GnomAD database, including 9,638 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 0.35 (9638 hom., cov: 32)
• Consequence: ENST00000701227.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

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 (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985152	XR_007066370.1	n.177+6343T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701227.1	n.134-3950T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53427 AN: 151970 Hom.: 9642 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.351 AC: 53456 AN: 152088 Hom.: 9638 Cov.: 32 AF XY: 0.351 AC XY: 26062 AN XY: 74328

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.370

Alfa AF: 0.377 Hom.: 17652

Bravo AF: 0.352

Asia WGS AF: 0.326 AC: 1133 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	0.95
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7244227; hg19: chr18-48549945;