chr6-89241194-A-G

Variant names:

• chr6-89241194-A-G
• rs1321355

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 0.344 in 152,152 control chromosomes in the GnomAD database, including 10,618 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 (10618 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.344 AC: 52327 AN: 152034 Hom.: 10598 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.344 AC: 52390 AN: 152152 Hom.: 10618 Cov.: 33 AF XY: 0.338 AC XY: 25146 AN XY: 74382

African (AFR) AF: 0.573 AC: 23789 AN: 41498

American (AMR) AF: 0.220 AC: 3360 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3468

East Asian (EAS) AF: 0.0774 AC: 401 AN: 5184

South Asian (SAS) AF: 0.227 AC: 1098 AN: 4832

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19056 AN: 67978

Other (OTH) AF: 0.287 AC: 607 AN: 2116

Alfa AF: 0.305 Hom.: 14979

Bravo AF: 0.346

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.76
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1321355; hg19: chr6-89950913; COSMIC: COSV69412405;