rs13098279

Positions:

• chr3-37190967-G-A
• chr3-37190967-G-C

Variant summary

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

The ENST00000702636.1(ENSG00000290046):​n.198-13708G>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 0.224 in 152,096 control chromosomes in the GnomAD database, including 4,354 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 0.22 (4354 hom., cov: 31)
• Consequence: ENST00000702636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377642	XR_007095869.1	n.111-13625G>A		intron_variant, non_coding_transcript_variant
LOC105377642	XR_002959625.2	n.208-13708G>A		intron_variant, non_coding_transcript_variant
LOC105377642	XR_007095870.1	n.208-13708G>A		intron_variant, non_coding_transcript_variant
LOC105377642	XR_007095871.1	n.111-13708G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702636.1	n.198-13708G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34046 AN: 151978 Hom.: 4356 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.224 AC: 34062 AN: 152096 Hom.: 4354 Cov.: 31 AF XY: 0.229 AC XY: 17059 AN XY: 74358

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.249

Alfa AF: 0.218 Hom.: 905

Bravo AF: 0.228

Asia WGS AF: 0.442 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13098279; hg19: chr3-37232458;