rs2486545

Positions:

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

Variant summary

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

The ENST00000441338.1(ENSG00000229960):​n.75-4908A>T 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 0.488 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: ENST00000441338.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000441338.1	n.75-4908A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.534

Alfa AF: 0.402 Hom.: 1202

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486545; hg19: chr1-244243575;