chr3-121427214-T-C

Position:

• chr3-121427214-T-C

Variant summary

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

The ENST00000666486.1(ENSG00000287022):​n.810+3175A>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 0.124 in 152,186 control chromosomes in the GnomAD database, including 1,285 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 0.12 (1285 hom., cov: 32)
• Consequence: ENST00000666486.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 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
	ENST00000666486.1	n.810+3175A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18853 AN: 152068 Hom.: 1284 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.124 AC: 18852 AN: 152186 Hom.: 1285 Cov.: 32 AF XY: 0.128 AC XY: 9497 AN XY: 74404

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.131

Alfa AF: 0.139 Hom.: 2582

Bravo AF: 0.116

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169302; hg19: chr3-121146061;