rs2486545

Variant names:

• chr1-244080273-T-A
• rs2486545
• ENST00000441338.1:n.75-4908A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-244080273-T-A
• chr1-244080273-T-C
• chr1-244080273-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441338.1(ENSG00000229960):​n.75-4908A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,048 control chromosomes in the GnomAD database, including 19,651 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 0.49 (19651 hom., cov: 32)
• Consequence: ENSG00000229960 ENST00000441338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 3 publications found

Genes affected

ENSG00000229960 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441338.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229960	ENST00000441338.1	TSL:3	n.75-4908A>T		intron	N/A
	ENSG00000229960	ENST00000746634.1		n.163+11316A>T		intron	N/A
	ENSG00000229960	ENST00000746635.1		n.103-4908A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74240 AN: 151930 Hom.: 19653 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.488 AC: 74270 AN: 152048 Hom.: 19651 Cov.: 32 AF XY: 0.484 AC XY: 35997 AN XY: 74308

African (AFR) AF: 0.298 AC: 12351 AN: 41484

American (AMR) AF: 0.595 AC: 9095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1393 AN: 5168

South Asian (SAS) AF: 0.570 AC: 2742 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5230 AN: 10558

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39500 AN: 67946

Other (OTH) AF: 0.534 AC: 1128 AN: 2114

Alfa AF: 0.402 Hom.: 1202

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.81
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2486545; hg19: chr1-244243575;