chr4-85418337-T-A

Variant names:

• chr4-85418337-T-A
• rs340191

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 0.342 in 152,032 control chromosomes in the GnomAD database, including 9,309 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 0.34 (9309 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51965 AN: 151914 Hom.: 9294 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.342 AC: 52020 AN: 152032 Hom.: 9309 Cov.: 31 AF XY: 0.338 AC XY: 25131 AN XY: 74310

African (AFR) AF: 0.270 AC: 11193 AN: 41496

American (AMR) AF: 0.368 AC: 5624 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5164

South Asian (SAS) AF: 0.180 AC: 869 AN: 4818

European-Finnish (FIN) AF: 0.375 AC: 3964 AN: 10562

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26814 AN: 67936

Other (OTH) AF: 0.360 AC: 761 AN: 2112

Alfa AF: 0.369 Hom.: 1318

Bravo AF: 0.343

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs340191; hg19: chr4-86339490;