chr4-65889542-C-G

Variant names:

• chr4-65889542-C-G
• rs11731436

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 0.333 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.332 AC: 13750 AN: 41460

American (AMR) AF: 0.342 AC: 5216 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3466

East Asian (EAS) AF: 0.188 AC: 970 AN: 5168

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4810

European-Finnish (FIN) AF: 0.277 AC: 2919 AN: 10526

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.347 AC: 23605 AN: 67936

Other (OTH) AF: 0.335 AC: 709 AN: 2114

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs11731436; hg19: chr4-66755260;