rs1553091

Positions:

• chr3-187999098-A-G
• chr3-187999098-A-T

Variant summary

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

The ENST00000415940.1(ENSG00000225058):​n.91-1340T>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 0.281 in 152,064 control chromosomes in the GnomAD database, including 6,520 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 0.28 (6520 hom., cov: 32)
• Consequence: ENST00000415940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986166	XR_001741061.2	n.416-1340T>C		intron_variant, non_coding_transcript_variant
LOC107986166	XR_001741062.2	n.317-1340T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415940.1	n.91-1340T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42655 AN: 151944 Hom.: 6518 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.281 AC: 42676 AN: 152064 Hom.: 6520 Cov.: 32 AF XY: 0.284 AC XY: 21138 AN XY: 74336

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.308

Alfa AF: 0.315 Hom.: 7088

Bravo AF: 0.273

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553091; hg19: chr3-187716886;