rs1468685

Variant names:

• chr2-190701045-A-T
• rs1468685
• ENST00000411949.5:n.84-1181T>A

Variant summary

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

The ENST00000411949.5(ENSG00000228509):​n.84-1181T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,996 control chromosomes in the GnomAD database, including 26,937 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 0.59 (26937 hom., cov: 31)
• Consequence: ENSG00000228509 ENST00000411949.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228509	ENST00000411949.5	n.84-1181T>A		intron_variant	Intron 1 of 2	3
ENSG00000228509	ENST00000428032.1	n.84+418T>A		intron_variant	Intron 1 of 2	3
ENSG00000228509	ENST00000676095.2	n.264-8310T>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89829 AN: 151878 Hom.: 26913 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.591 AC: 89899 AN: 151996 Hom.: 26937 Cov.: 31 AF XY: 0.595 AC XY: 44171 AN XY: 74272

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.600

Alfa AF: 0.606 Hom.: 3491

Bravo AF: 0.570

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468685; hg19: chr2-191565771;