rs4105144

Variant names:

• chr19-40852719-T-C
• rs4105144
• ENST00000601627.1:n.118-39272T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000601627.1(ENSG00000268797):​n.118-39272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.44 (3619 hom., cov: 39)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 58 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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.118-39272T>C		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 66450 AN: 150086 Hom.: 3617 Cov.: 39

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.443

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.443 AC: 66479 AN: 150196 Hom.: 3619 Cov.: 39 AF XY: 0.442 AC XY: 32380 AN XY: 73308

African (AFR) AF: 0.389 AC: 15900 AN: 40886

American (AMR) AF: 0.465 AC: 7002 AN: 15062

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1702 AN: 3442

East Asian (EAS) AF: 0.401 AC: 1992 AN: 4962

South Asian (SAS) AF: 0.405 AC: 1919 AN: 4742

European-Finnish (FIN) AF: 0.490 AC: 5093 AN: 10386

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31349 AN: 67430

Other (OTH) AF: 0.442 AC: 922 AN: 2084

Alfa AF: 0.458 Hom.: 538

Asia WGS AF: 0.395 AC: 1360 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4105144; hg19: chr19-41358624;