rs1603225

Positions:

• chr12-70488947-T-C

Variant summary

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

The ENST00000548687.5(ENSG00000258168):​n.243+20620T>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 0.156 in 146,690 control chromosomes in the GnomAD database, including 2,103 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 0.16 (2103 hom., cov: 32)
• Consequence: ENST00000548687.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369828	XR_001749196.2	n.250-18948T>C		intron_variant, non_coding_transcript_variant
LOC105369828	XR_007063360.1	n.250-18948T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000548687.5	n.243+20620T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 22907 AN: 146574 Hom.: 2103 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00126

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.156 AC: 22904 AN: 146690 Hom.: 2103 Cov.: 32 AF XY: 0.153 AC XY: 10886 AN XY: 71298

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00126

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.145

Alfa AF: 0.194 Hom.: 1820

Bravo AF: 0.145

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1603225; hg19: chr12-70882727;