rs6852535

Variant names:

• chr4-122557561-G-A
• rs6852535

Your query was ambiguous. Multiple possible variants found:

• chr4-122557561-G-A
• chr4-122557561-G-C

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 0.25 in 152,096 control chromosomes in the GnomAD database, including 5,768 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 0.25 (5768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 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: 0.250 AC: 37953 AN: 151978 Hom.: 5755 Cov.: 31

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.250 AC: 37986 AN: 152096 Hom.: 5768 Cov.: 31 AF XY: 0.255 AC XY: 18974 AN XY: 74334

African (AFR) AF: 0.0742 AC: 3080 AN: 41522

American (AMR) AF: 0.298 AC: 4548 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1487 AN: 3462

East Asian (EAS) AF: 0.347 AC: 1791 AN: 5158

South Asian (SAS) AF: 0.506 AC: 2440 AN: 4824

European-Finnish (FIN) AF: 0.292 AC: 3089 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20445 AN: 67974

Other (OTH) AF: 0.303 AC: 639 AN: 2112

Alfa AF: 0.290 Hom.: 22932

Bravo AF: 0.238

Asia WGS AF: 0.425 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6852535; hg19: chr4-123478716;