chr3-40859765-C-T

Position:

• chr3-40859765-C-T

Variant summary

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

The ENST00000412811.1(ENSG00000231873):​n.266-2627C>T 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 0.0835 in 152,238 control chromosomes in the GnomAD database, including 876 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 0.083 (876 hom., cov: 33)
• Consequence: ENST00000412811.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377043	XR_007095885.1	n.266-51183C>T		intron_variant, non_coding_transcript_variant
LOC105377043	XR_940766.3	n.266-10119C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412811.1	n.266-2627C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12671 AN: 152120 Hom.: 869 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0738

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0835 AC: 12707 AN: 152238 Hom.: 876 Cov.: 33 AF XY: 0.0809 AC XY: 6021 AN XY: 74450

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0475 Hom.: 264

Bravo AF: 0.0923

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.5
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514703; hg19: chr3-40901256;