chr4-138888027-G-A

Variant names:

• chr4-138888027-G-A
• rs77803164
• ENST00000505607.2:n.203+22047C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505607.2(ENSG00000250195):​n.203+22047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,066 control chromosomes in the GnomAD database, including 164 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 0.043 (164 hom., cov: 31)
• Consequence: ENSG00000250195 ENST00000505607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 2 publications found

Genes affected

ENSG00000250195 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505607.2. 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
	LOC105377448	NR_133945.1		n.162-67950C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250195	ENST00000505607.2	TSL:2	n.203+22047C>T		intron	N/A
	ENSG00000250195	ENST00000507038.1	TSL:5	n.159-42654C>T		intron	N/A
	ENSG00000250195	ENST00000511951.2	TSL:3	n.484-67950C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6473 AN: 151948 Hom.: 164 Cov.: 31

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0202

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0513

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

GnomAD4 genome AF: 0.0426 AC: 6474 AN: 152066 Hom.: 164 Cov.: 31 AF XY: 0.0398 AC XY: 2961 AN XY: 74320

African (AFR) AF: 0.0190 AC: 789 AN: 41486

American (AMR) AF: 0.0368 AC: 562 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0583 AC: 202 AN: 3466

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5168

South Asian (SAS) AF: 0.0208 AC: 100 AN: 4808

European-Finnish (FIN) AF: 0.0451 AC: 477 AN: 10574

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0606 AC: 4122 AN: 67980

Other (OTH) AF: 0.0508 AC: 107 AN: 2108

Alfa AF: 0.0468 Hom.: 62

Bravo AF: 0.0421

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.76
PhyloP100		-2.7

Splicing

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: rs77803164;

hg19: chr4-139809181;