rs6856616

Variant names:

• chr4-38323415-T-C
• rs6856616

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 0.149 in 152,242 control chromosomes in the GnomAD database, including 2,469 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 0.15 (2469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.149 AC: 22646 AN: 152124 Hom.: 2469 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.149 AC: 22659 AN: 152242 Hom.: 2469 Cov.: 33 AF XY: 0.150 AC XY: 11142 AN XY: 74434

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0861 Hom.: 1394

Bravo AF: 0.161

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6856616; hg19: chr4-38325036;