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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902534	XR_007062358.1	n.167-1821T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234580	ENST00000456722.1	n.156-1821T>C		intron_variant	Intron 1 of 1	3

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 v4.3

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

Other links and lift over

dbSNP: rs2061971; hg19: chr10-45089053;