rs2061971

Variant names:

• chr10-44593605-A-G
• rs2061971
• ENST00000456722.1:n.156-1821T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-44593605-A-G
• chr10-44593605-A-T

Variant summary

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

The ENST00000456722.1(ENSG00000234580):​n.156-1821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,746 control chromosomes in the GnomAD database, including 18,033 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 0.48 (18033 hom., cov: 31)
• Consequence: ENSG00000234580 ENST00000456722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

Genes affected

ENSG00000234580 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456722.1. 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
	ENSG00000234580	ENST00000456722.1	TSL:3	n.156-1821T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73437 AN: 151628 Hom.: 17999 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.485 AC: 73531 AN: 151746 Hom.: 18033 Cov.: 31 AF XY: 0.488 AC XY: 36205 AN XY: 74146

African (AFR) AF: 0.443 AC: 18295 AN: 41344

American (AMR) AF: 0.515 AC: 7852 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3468

East Asian (EAS) AF: 0.525 AC: 2700 AN: 5140

South Asian (SAS) AF: 0.538 AC: 2588 AN: 4806

European-Finnish (FIN) AF: 0.558 AC: 5878 AN: 10528

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33128 AN: 67914

Other (OTH) AF: 0.476 AC: 1005 AN: 2110

Alfa AF: 0.476 Hom.: 4147

Bravo AF: 0.484

Asia WGS AF: 0.558 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.44
PhyloP100		-1.2

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: rs2061971;

hg19: chr10-45089053;