4-162775194-C-T

Variant names:

• chr4-162775194-C-T
• rs1458151
• ENST00000661387.1:n.165+33415C>T

Variant summary

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

The ENST00000661387.1(ENSG00000248431):​n.165+33415C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,120 control chromosomes in the GnomAD database, including 70,445 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 0.96 (70445 hom., cov: 32)
• Consequence: ENSG00000248431 ENST00000661387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 1 publications found

Genes affected

ENSG00000248431 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661387.1. 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
	ENSG00000248431	ENST00000661387.1		n.165+33415C>T		intron	N/A
	ENSG00000248431	ENST00000728266.1		n.185+33415C>T		intron	N/A
	ENSG00000248431	ENST00000728267.1		n.536-10071C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146248 AN: 152002 Hom.: 70407 Cov.: 32

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.962 AC: 146342 AN: 152120 Hom.: 70445 Cov.: 32 AF XY: 0.964 AC XY: 71653 AN XY: 74360

African (AFR) AF: 0.929 AC: 38574 AN: 41538

American (AMR) AF: 0.971 AC: 14793 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3463 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5143 AN: 5178

South Asian (SAS) AF: 0.977 AC: 4719 AN: 4828

European-Finnish (FIN) AF: 0.978 AC: 10378 AN: 10614

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66028 AN: 67948

Other (OTH) AF: 0.969 AC: 2043 AN: 2108

Alfa AF: 0.971 Hom.: 86220

Bravo AF: 0.962

Asia WGS AF: 0.968 AC: 3364 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.28

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: rs1458151;

hg19: chr4-163696346;