rs4443878

chr1-240741118-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000431139.4(ENSG00000230015):n.315-1265G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 152,230 control chromosomes in the GnomAD database, including 42 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 0.020 (42 hom., cov: 33)
• Consequence: ENST00000431139.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0198 (3014/152230) while in subpopulation NFE AF= 0.028 (1905/68008). AF 95% confidence interval is 0.027. There are 42 homozygotes in gnomad4. There are 1437 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 42 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506929	XR_159119.5	n.61-1265G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000431139.4	n.315-1265G>A		intron_variant, non_coding_transcript_variant
	ENST00000688796.1	n.540-1265G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0198 AC: 3011 AN: 152112 Hom.: 42 Cov.: 33

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0161

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0198 AC: 3014 AN: 152230 Hom.: 42 Cov.: 33 AF XY: 0.0193 AC XY: 1437 AN XY: 74444

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0185

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0245 Hom.: 35

Bravo AF: 0.0186

Asia WGS AF: 0.00924 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4443878; hg19: chr1-240904418;