rs4075749

Positions:

• chr3-30437405-A-G

Variant summary

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

The ENST00000691186.1(ENSG00000289450):​n.213-31628A>G 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 0.238 in 152,010 control chromosomes in the GnomAD database, including 4,828 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 0.24 (4828 hom., cov: 31)
• Consequence: ENST00000691186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

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 (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377013	XR_940683.2	n.293+3602T>C		intron_variant, non_coding_transcript_variant
LOC101927995	XR_001740627.2	n.213-31628A>G		intron_variant, non_coding_transcript_variant
LOC101927995	XR_001740628.2	n.261-31628A>G		intron_variant, non_coding_transcript_variant
LOC101927995	XR_007095856.1	n.257-31628A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691186.1	n.213-31628A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36232 AN: 151892 Hom.: 4828 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.238 AC: 36229 AN: 152010 Hom.: 4828 Cov.: 31 AF XY: 0.235 AC XY: 17465 AN XY: 74278

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.248

Alfa AF: 0.292 Hom.: 6598

Bravo AF: 0.231

Asia WGS AF: 0.135 AC: 472 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	0.28
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075749; hg19: chr3-30478897;