3-114218488-G-A

Position:

• chr3-114218488-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000493033.1(ENSG00000241490):​n.160+3938G>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 0.0298 in 152,246 control chromosomes in the GnomAD database, including 93 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 0.030 (93 hom., cov: 32)
• Consequence: ENST00000493033.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4542/152246) while in subpopulation NFE AF= 0.0474 (3226/67994). AF 95% confidence interval is 0.0461. There are 93 homozygotes in gnomad4. There are 1956 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 93 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000493033.1	n.160+3938G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000481773.1	n.238+3938G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4541 AN: 152128 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00871

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0474

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0298 AC: 4542 AN: 152246 Hom.: 93 Cov.: 32 AF XY: 0.0263 AC XY: 1956 AN XY: 74456

Gnomad4 AFR AF: 0.00871

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00560

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0474

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0474 Hom.: 277

Bravo AF: 0.0321

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.2
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9846423; hg19: chr3-113937335;