4-154142036-C-T

Variant names:

• chr4-154142036-C-T
• rs4611909
• ENST00000624941.4:n.180-80C>T

Variant summary

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

The ENST00000624941.4(ENSG00000280241):​n.180-80C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,168 control chromosomes in the GnomAD database, including 63,165 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 0.90 (63164 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000280241 ENST00000624941.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 1 publications found

Genes affected

ENSG00000280241 (HGNC:58900):

LOC101927947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624941.4. 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
	ENSG00000280241	ENST00000624941.4	TSL:3	n.180-80C>T		intron	N/A
	ENSG00000280241	ENST00000660197.1		n.200-80C>T		intron	N/A
	ENSG00000280241	ENST00000839747.1		n.720-80C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137322 AN: 152048 Hom.: 63131 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.911

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.903 AC: 137401 AN: 152166 Hom.: 63164 Cov.: 31 AF XY: 0.905 AC XY: 67355 AN XY: 74390

African (AFR) AF: 0.706 AC: 29290 AN: 41460

American (AMR) AF: 0.956 AC: 14618 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3259 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5180

South Asian (SAS) AF: 0.993 AC: 4790 AN: 4822

European-Finnish (FIN) AF: 0.969 AC: 10272 AN: 10606

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66919 AN: 68026

Other (OTH) AF: 0.912 AC: 1924 AN: 2110

Alfa AF: 0.929 Hom.: 8604

Bravo AF: 0.891

Asia WGS AF: 0.973 AC: 3378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.082
DANN	Benign	0.44
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4611909; hg19: chr4-155063188;