rs1468685

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000428032.2	n.307+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

African (AFR) AF: 0.583 AC: 24159 AN: 41456

American (AMR) AF: 0.495 AC: 7560 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2241 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1739 AN: 5172

South Asian (SAS) AF: 0.631 AC: 3041 AN: 4820

European-Finnish (FIN) AF: 0.726 AC: 7661 AN: 10548

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.611 AC: 41532 AN: 67948

Other (OTH) AF: 0.600 AC: 1267 AN: 2112

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1468685; hg19: chr2-191565771;