3-41094730-C-CCAACCTGGATT

Variant names:

• chr3-41094730-C-CCAACCTGGATT
• rs2067235
• ENST00000808368.1:n.394+1819_394+1820insAATCCAGGTTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000808368.1(ENSG00000305067):​n.394+1819_394+1820insAATCCAGGTTG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18283 hom., cov: 0)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 5 publications found

Genes affected

ENSG00000305067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808368.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305067	ENST00000808368.1		n.394+1819_394+1820insAATCCAGGTTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73102 AN: 151566 Hom.: 18271 Cov.: 0

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.482 AC: 73156 AN: 151684 Hom.: 18283 Cov.: 0 AF XY: 0.477 AC XY: 35323 AN XY: 74122

African (AFR) AF: 0.395 AC: 16342 AN: 41374

American (AMR) AF: 0.434 AC: 6625 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1436 AN: 3464

East Asian (EAS) AF: 0.359 AC: 1845 AN: 5136

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4814

European-Finnish (FIN) AF: 0.591 AC: 6216 AN: 10526

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37413 AN: 67812

Other (OTH) AF: 0.484 AC: 1020 AN: 2108

Alfa AF: 0.504 Hom.: 2098

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2067235; hg19: chr3-41136221;