chr4-65889542-C-G

Variant names:

• chr4-65889542-C-G
• rs11731436

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.333 in 151,922 control chromosomes in the GnomAD database, including 8,563 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 0.33 (8563 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50524 AN: 151804 Hom.: 8551 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.333 AC: 50560 AN: 151922 Hom.: 8563 Cov.: 31 AF XY: 0.329 AC XY: 24402 AN XY: 74226

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.335

Alfa AF: 0.351 Hom.: 1144

Bravo AF: 0.340

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11731436; hg19: chr4-66755260;