rs1164064

Positions:

• chr3-109743553-G-A

Variant summary

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

The ENST00000485384.1(ENSG00000242029):​n.30-61229G>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 0.399 in 151,898 control chromosomes in the GnomAD database, including 12,221 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 0.40 (12221 hom., cov: 32)
• Consequence: ENST00000485384.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) 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
LOC124906267	XR_007096002.1	n.154+63358G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000485384.1	n.30-61229G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60617 AN: 151778 Hom.: 12208 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.399 AC: 60673 AN: 151898 Hom.: 12221 Cov.: 32 AF XY: 0.394 AC XY: 29269 AN XY: 74218

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.415

Alfa AF: 0.419 Hom.: 16991

Bravo AF: 0.397

Asia WGS AF: 0.357 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1164064; hg19: chr3-109462400;