19-40868653-CAA-CAAAAA

Variant names:

• chr19-40868653-C-CAAA
• rs34226463
• ENST00000601627.1:n.118-23338_118-23337insAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000601627.1(ENSG00000268797):​n.118-23338_118-23337insAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0018 (9 hom., cov: 0)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 2 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

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

• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00181 (256/141198) while in subpopulation SAS AF = 0.0261 (113/4334). AF 95% confidence interval is 0.0222. There are 9 homozygotes in GnomAd4. There are 147 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268797	ENST00000601627.1	n.118-23338_118-23337insAAA		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.00183 AC: 258 AN: 141144 Hom.: 9 Cov.: 0

Gnomad AFR AF: 0.000932

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00107

Gnomad ASJ AF: 0.00390

Gnomad EAS AF: 0.000441

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.000237

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.00365

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

GnomAD4 genome AF: 0.00181 AC: 256 AN: 141198 Hom.: 9 Cov.: 0 AF XY: 0.00216 AC XY: 147 AN XY: 68158

African (AFR) AF: 0.000929 AC: 36 AN: 38732

American (AMR) AF: 0.00106 AC: 15 AN: 14102

Ashkenazi Jewish (ASJ) AF: 0.00390 AC: 13 AN: 3332

East Asian (EAS) AF: 0.000443 AC: 2 AN: 4518

South Asian (SAS) AF: 0.0261 AC: 113 AN: 4334

European-Finnish (FIN) AF: 0.000237 AC: 2 AN: 8422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 274

European-Non Finnish (NFE) AF: 0.00105 AC: 68 AN: 64658

Other (OTH) AF: 0.00363 AC: 7 AN: 1928

Alfa AF: 0.000398 Hom.: 1219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs34226463; hg19: chr19-41374558;