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:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927947	XR_007058335.1	n.393-80C>T		intron_variant	Intron 2 of 5
LOC101927947	XR_007058336.1	n.3959-80C>T		intron_variant	Intron 9 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280241	ENST00000624941.4	n.180-80C>T		intron_variant	Intron 1 of 5	3
ENSG00000280241	ENST00000660197.1	n.200-80C>T		intron_variant	Intron 2 of 4
ENSG00000280241	ENST00000839747.1	n.720-80C>T		intron_variant	Intron 7 of 8
ENSG00000280241	ENST00000839753.1	n.333-80C>T		intron_variant	Intron 1 of 1

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 v4.3

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;