3-188022735-T-C

Variant names:

• chr3-188022735-T-C
• rs6808574
• XR_001741061.2:n.163-18747A>G

Variant summary

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

The XR_001741061.2(LOC107986166):​n.163-18747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,102 control chromosomes in the GnomAD database, including 34,725 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 0.67 (34725 hom., cov: 32)
• Consequence: LOC107986166 XR_001741061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 55 publications found

Genes affected

LOC107986166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986166	XR_001741061.2	n.163-18747A>G		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101757 AN: 151984 Hom.: 34681 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.670 AC: 101856 AN: 152102 Hom.: 34725 Cov.: 32 AF XY: 0.676 AC XY: 50243 AN XY: 74362

African (AFR) AF: 0.710 AC: 29443 AN: 41468

American (AMR) AF: 0.733 AC: 11206 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5151 AN: 5178

South Asian (SAS) AF: 0.789 AC: 3813 AN: 4832

European-Finnish (FIN) AF: 0.604 AC: 6383 AN: 10564

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41732 AN: 67990

Other (OTH) AF: 0.665 AC: 1404 AN: 2112

Alfa AF: 0.639 Hom.: 98472

Bravo AF: 0.679

Asia WGS AF: 0.885 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.53
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6808574; hg19: chr3-187740523; COSMIC: COSV55129687;