2-84217762-A-G

Variant names:

• chr2-84217762-A-G
• rs6547537
• XR_001739572.1:n.72-12734T>C

Variant summary

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

The XR_001739572.1(LOC107985905):​n.72-12734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,034 control chromosomes in the GnomAD database, including 38,895 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 0.71 (38895 hom., cov: 32)
• Consequence: LOC107985905 XR_001739572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 7 publications found

Genes affected

LOC107985905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985905	XR_001739572.1	n.72-12734T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107230 AN: 151916 Hom.: 38863 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.706 AC: 107310 AN: 152034 Hom.: 38895 Cov.: 32 AF XY: 0.712 AC XY: 52926 AN XY: 74334

African (AFR) AF: 0.518 AC: 21452 AN: 41410

American (AMR) AF: 0.754 AC: 11525 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2803 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4579 AN: 5168

South Asian (SAS) AF: 0.803 AC: 3867 AN: 4816

European-Finnish (FIN) AF: 0.777 AC: 8224 AN: 10578

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52404 AN: 67980

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.676 Hom.: 17056

Bravo AF: 0.695

Asia WGS AF: 0.811 AC: 2819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6547537; hg19: chr2-84444886;