chr1-72887645-A-T

Variant names:

• chr1-72887645-A-T
• rs6657082
• ENST00000445976.1:n.229+11122T>A

Variant summary

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

The ENST00000445976.1(ENSG00000225087):​n.229+11122T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,906 control chromosomes in the GnomAD database, including 15,101 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 0.44 (15101 hom., cov: 32)
• Consequence: ENSG00000225087 ENST00000445976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 3 publications found

Genes affected

ENSG00000225087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445976.1. 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
	ENSG00000225087	ENST00000445976.1	TSL:3	n.229+11122T>A		intron	N/A
	ENSG00000225087	ENST00000654386.1		n.325+11122T>A		intron	N/A
	ENSG00000225087	ENST00000656766.1		n.474+11122T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66520 AN: 151788 Hom.: 15101 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.438 AC: 66550 AN: 151906 Hom.: 15101 Cov.: 32 AF XY: 0.442 AC XY: 32832 AN XY: 74246

African (AFR) AF: 0.356 AC: 14740 AN: 41448

American (AMR) AF: 0.399 AC: 6085 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3466

East Asian (EAS) AF: 0.720 AC: 3716 AN: 5162

South Asian (SAS) AF: 0.572 AC: 2753 AN: 4814

European-Finnish (FIN) AF: 0.441 AC: 4647 AN: 10542

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31307 AN: 67902

Other (OTH) AF: 0.467 AC: 984 AN: 2108

Alfa AF: 0.439 Hom.: 1864

Bravo AF: 0.428

Asia WGS AF: 0.615 AC: 2137 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.61
PhyloP100		0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6657082;

hg19: chr1-73353328;