chr4-181406715-G-A

Variant names:

• chr4-181406715-G-A
• rs724657
• XR_007058402.1:n.78-12141C>T

Variant summary

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

The XR_007058402.1(LOC124900822):​n.78-12141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,946 control chromosomes in the GnomAD database, including 7,517 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 0.30 (7517 hom., cov: 32)
• Consequence: LOC124900822 XR_007058402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 3 publications found

Genes affected

LOC124900822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.298 AC: 45243 AN: 151828 Hom.: 7512 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.298 AC: 45256 AN: 151946 Hom.: 7517 Cov.: 32 AF XY: 0.306 AC XY: 22703 AN XY: 74268

African (AFR) AF: 0.134 AC: 5574 AN: 41456

American (AMR) AF: 0.335 AC: 5118 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1869 AN: 5148

South Asian (SAS) AF: 0.490 AC: 2361 AN: 4818

European-Finnish (FIN) AF: 0.393 AC: 4143 AN: 10540

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23856 AN: 67930

Other (OTH) AF: 0.308 AC: 651 AN: 2112

Alfa AF: 0.335 Hom.: 28709

Bravo AF: 0.286

Asia WGS AF: 0.414 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs724657; hg19: chr4-182327868;