rs4431886

chr1-56386595-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641035.1(ENSG00000260971):n.555+90538A>G 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 0.188 in 152,198 control chromosomes in the GnomAD database, including 4,112 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 0.19 (4112 hom., cov: 32)
• Consequence: ENST00000641035.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641035.1	n.555+90538A>G		intron_variant, non_coding_transcript_variant
	ENST00000641346.1	c.*269+13499A>G		intron_variant, NMD_transcript_variant				A2
	ENST00000641415.1	c.*95+96668A>G		intron_variant, NMD_transcript_variant				A2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28632 AN: 152080 Hom.: 4105 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.188 AC: 28683 AN: 152198 Hom.: 4112 Cov.: 32 AF XY: 0.184 AC XY: 13717 AN XY: 74416

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.0739

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.154

Alfa AF: 0.117 Hom.: 1721

Bravo AF: 0.200

Asia WGS AF: 0.110 AC: 383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.8
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4431886; hg19: chr1-56852267;