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: 59 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. 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
	ENSG00000268797	ENST00000601627.1	TSL:3	n.118-39272T>C		intron	N/A	ENSP00000469533.1	M0QY20

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4105144;

hg19: chr19-41358624;