4-64789270-A-G

Variant names:

• chr4-64789270-A-G
• rs11731709
• XR_001741711.2:n.204+14445A>G

Variant summary

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

The XR_001741711.2(LOC107986284):​n.204+14445A>G variant causes a intron change. The variant allele was found at a frequency of 0.218 in 152,004 control chromosomes in the GnomAD database, including 4,082 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 0.22 (4082 hom., cov: 32)
• Consequence: LOC107986284 XR_001741711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02
• Publications: 2 publications found

Genes affected

LOC107986284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33141 AN: 151886 Hom.: 4088 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.218 AC: 33138 AN: 152004 Hom.: 4082 Cov.: 32 AF XY: 0.223 AC XY: 16537 AN XY: 74296

African (AFR) AF: 0.125 AC: 5190 AN: 41518

American (AMR) AF: 0.322 AC: 4912 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2358 AN: 5150

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2269 AN: 10574

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15160 AN: 67916

Other (OTH) AF: 0.259 AC: 546 AN: 2106

Alfa AF: 0.225 Hom.: 8740

Bravo AF: 0.222

Asia WGS AF: 0.369 AC: 1285 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs11731709; hg19: chr4-65654988;