chr4-110736347-T-A

Variant names:

• chr4-110736347-T-A
• rs4307025

Variant summary

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

The variant allele was found at a frequency of 0.375 in 151,954 control chromosomes in the GnomAD database, including 11,651 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 0.38 (11651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 6 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56979 AN: 151836 Hom.: 11622 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.375 AC: 57051 AN: 151954 Hom.: 11651 Cov.: 31 AF XY: 0.389 AC XY: 28883 AN XY: 74278

African (AFR) AF: 0.449 AC: 18602 AN: 41442

American (AMR) AF: 0.474 AC: 7234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1654 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3776 AN: 5170

South Asian (SAS) AF: 0.393 AC: 1889 AN: 4810

European-Finnish (FIN) AF: 0.355 AC: 3726 AN: 10498

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18999 AN: 67974

Other (OTH) AF: 0.370 AC: 780 AN: 2110

Alfa AF: 0.182 Hom.: 344

Bravo AF: 0.389

Asia WGS AF: 0.542 AC: 1876 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.47
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4307025; hg19: chr4-111657503;