chr3-101888320-A-G

Position:

• chr3-101888320-A-G

Variant summary

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

The ENST00000657494.1(ENSG00000287682):​n.226+1488A>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 0.255 in 152,132 control chromosomes in the GnomAD database, including 5,170 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 0.26 (5170 hom., cov: 32)
• Consequence: ENST00000657494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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 (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657494.1	n.226+1488A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38752 AN: 152014 Hom.: 5158 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0939

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.255 AC: 38802 AN: 152132 Hom.: 5170 Cov.: 32 AF XY: 0.256 AC XY: 19040 AN XY: 74350

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0941

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.264

Alfa AF: 0.252 Hom.: 9867

Bravo AF: 0.260

Asia WGS AF: 0.217 AC: 755 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	0.32
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17842780; hg19: chr3-101607164; COSMIC: COSV53460789;